Practical — Genome-Wide Association Study (GWAS)¶
In this practical you will learn the essentials of running a Genome-Wide Association Study (GWAS), along with common pitfalls to avoid.
We will work entirely from the command line (Calysto Bash terminals) for data processing with PLINK/REGENIE/LOCUSZOOM, and switch to R/Python for visualisation.
- PLINK documentation
How this notebook is organised¶
Each cell is either:
- Markdown text – like the block you are reading now.
- Calysto Bash cell – runs Linux shell commands (labelled “Calysto Bash” at top-right).
- R cell – runs R code (labelled “R4.4”).
- Python cell – runs Python code (labelled “Python 3.12”).
Running cells¶
| Action | Windows / Linux | macOS |
|---|---|---|
| Run selected cell | Shift + Enter | Cmd + Enter |
| Re-run after editing | Ctrl + Enter | Cmd + Enter |
Tip: click inside a code cell before executing it.
Let’s start by inspecting your home directory.
In the Calysto Bash cell below, list its contents:
# List files in your home folder
ls ~/
GWASintro_2025_REGENIE.ipynb output __pycache__
# create the output folder for storing output files
if [ ! -d ./output ]; then
mkdir ./output
fi
List the content of the data folder that you will used next:
ls /home/student/USER/GWAS/data/
anno_file.txt covar_2024_imp_2046_phenotype.txt covar_2024_imp_2046.txt covar_2024_WES_1826_covars.txt covar_2024_WES_1826_phenotype.txt covar_2024_WES_1826.txt covar_PCs.txt European_1w.bed European_1w.bim European_1w.eigenval European_1w.eigenvec European_1w.fam European_1w_fig.eigenvec European_1w_pca.txt European_1w.ped European_1w_phenotypes.txt European_1w_QC.bed European_1w_QC.bim European_1w_QC.fam European_1w_QC_PC20.assoc.linear European_1w_QC_PC20.assoc.linear.adjusted European_1w_QC_PC20.txt European_1w_smartpca.par mask_file.txt phenotype.txt plotPCA.py plotPlink.py plotPlink.R regenie_anno_file_SNP.txt regenie_mask_file.txt regenie_set_list_CHR_POS.txt set_list.txt ukb23150_c1_c22_2024_WES_1826_QCpruned.bed ukb23150_c1_c22_2024_WES_1826_QCpruned.bim ukb23150_c1_c22_2024_WES_1826_QCpruned.fam ukb23150_c22_2024_WES_1826.bed ukb23150_c22_2024_WES_1826.bim ukb23150_c22_2024_WES_1826.fam ukb_imp_ALL_22_chr_trans_2024_imp_2046_QCpruned.bed ukb_imp_ALL_22_chr_trans_2024_imp_2046_QCpruned.bim ukb_imp_ALL_22_chr_trans_2024_imp_2046_QCpruned.fam ukb_imp_ALL_trans_c22_2024_imp_2046.bed ukb_imp_ALL_trans_c22_2024_imp_2046.bim ukb_imp_ALL_trans_c22_2024_imp_2046.fam v1_backup_20250713 v2_backup_20250718
Exercise A: running your first GWAS¶
We're using simnulated UKBiobank data!!!
Briefly, the GWAS data consist of SNP genotyping data from 10,000 European individuals (someone tells you that they are Europeans but you have to check by yourself) with information about their standing height (in meters).
To make sure the GWAS analyses will run fast the main data file (European_1w.bed) is in a binary format, which is not very reader friendly.
However, PLINK (the program we will use to run the analyses) will print summary statistics about the data (number of SNPs, number of individuals etc) to the screen when you run an analysis.
Also, there are two additional data files, European_1w.bim and European_1w.fam, which are not in binary format and which contains information about the SNPs in the data and the individuals in the data, respectively.
(You can read more about the data format in the manuals linked to above - but for now this is all you need to know).
Let's look inside the .fam file, which contains information about the individuals. The head and tail commands shows the first and last 10 lines of the file. Try to run them:
Note:¶
These 1w European samples were randomly sampled from the whole UKB cohort using stratified random sampling, in which 30% were sampled from the European population and the rest 70% sampled from the non-European population.
#head prints the 10 lines of the fam file
head /home/student/USER/GWAS/data/European_1w.fam
echo "-------------"
#tail prints the last 10 lines of the fam file
tail /home/student/USER/GWAS/data/European_1w.fam
1000992 1000992 0 0 1 1.68 1001118 1001118 0 0 1 1.61 1002621 1002621 0 0 2 1.5 1002993 1002993 0 0 2 1.57 1003258 1003258 0 0 2 1.64 1004181 1004181 0 0 2 1.76 1004240 1004240 0 0 1 1.62 1004285 1004285 0 0 1 1.66 1005685 1005685 0 0 2 1.58 1006795 1006795 0 0 2 1.55 ------------- 6022702 6022702 0 0 2 1.74 6022727 6022727 0 0 1 1.73 6023248 6023248 0 0 2 1.55 6023752 6023752 0 0 2 1.69 6024345 6024345 0 0 2 1.62 6024403 6024403 0 0 1 1.7 6024436 6024436 0 0 1 1.8 6024522 6024522 0 0 1 1.88 6024942 6024942 0 0 2 1.7 6025409 6025409 0 0 2 1.54
data <-read.table("/home/student/USER/GWAS/data/European_1w.fam")
str(data)
hist(as.numeric(data$V6),main="Standing Height")
'data.frame': 10000 obs. of 6 variables: $ V1: int 1000992 1001118 1002621 1002993 1003258 1004181 1004240 1004285 1005685 1006795 ... $ V2: int 1000992 1001118 1002621 1002993 1003258 1004181 1004240 1004285 1005685 1006795 ... $ V3: int 0 0 0 0 0 0 0 0 0 0 ... $ V4: int 0 0 0 0 0 0 0 0 0 0 ... $ V5: int 1 1 2 2 2 2 1 1 2 2 ... $ V6: num 1.68 1.61 1.5 1.57 1.64 1.76 1.62 1.66 1.58 1.55 ...
#head prints the 10 lines of the bim file
head /home/student/USER/GWAS/data/European_1w.bim|column -t
echo "-------------"
#tail prints the last 10 lines of the bim file
tail /home/student/USER/GWAS/data/European_1w.bim|column -t
1 rs28659788 0 723307 G C 1 rs116587930 0 727841 A G 1 rs116720794 0 729632 T C 1 rs3131972 0 752721 A G 1 rs12184325 0 754105 T C 1 rs3131962 0 756604 A G 1 rs114525117 0 759036 A G 1 rs3115850 0 761147 T C 1 rs115991721 0 767096 G A 1 rs12562034 0 768448 A G ------------- 22 rs73174437 0 51177257 T C 22 Affx-89025365 0 51178285 A AC 22 Affx-89011903 0 51183153 T TG 22 rs140584689 0 51183253 A G 22 rs5771002 0 51183255 A G 22 rs3865764 0 51185848 G A 22 rs142680588 0 51193629 G A 22 rs9616974 0 51217954 A G 22 rs116656403 0 51224208 A G 22 rs149733995 0 51238249 A C
# Because we can not directly view a binary file, we convert the European_1w.bed file to the European_1w.ped to learn the content within it
# Command for the convertion: plink --bfile /home/student/USER/GWAS/data/European_1w --recode tab --memory 5000 --out /home/student/USER/GWAS/data/test
# print the 20 rows of the ped file which is reader-friendly
echo 'sample-info columns (1-6) and three SNP (7-8, 9-10, 11-12)'
head -n 20 /home/student/USER/GWAS/data/European_1w.ped |
awk '{print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}'
sample-info columns (1-6) and three SNP (7-8, 9-10, 11-12) 1000992 1000992 0 0 1 1.68 0 0 G G C C 1001118 1001118 0 0 1 1.61 0 0 G G C C 1002621 1002621 0 0 2 1.5 0 0 G G 0 0 1002993 1002993 0 0 2 1.57 0 0 G G C C 1003258 1003258 0 0 2 1.64 0 0 G G C C 1004181 1004181 0 0 2 1.76 0 0 G G C C 1004240 1004240 0 0 1 1.62 0 0 G G T C 1004285 1004285 0 0 1 1.66 0 0 G G C C 1005685 1005685 0 0 2 1.58 0 0 G G C C 1006795 1006795 0 0 2 1.55 0 0 G G C C 1006840 1006840 0 0 1 1.7 0 0 G G C C 1007533 1007533 0 0 1 1.667 C C G G C C 1007571 1007571 0 0 2 1.74 C C G G C C 1008723 1008723 0 0 2 1.63 0 0 G G C C 1010985 1010985 0 0 1 1.7 0 0 G G C C 1011289 1011289 0 0 1 1.88 0 0 G G C C 1012247 1012247 0 0 1 1.8 0 0 0 0 C C 1012361 1012361 0 0 1 1.77 0 0 G G C C 1012528 1012528 0 0 2 1.57 0 0 G G C C 1013817 1013817 0 0 2 1.62 0 0 0 0 C C
Let's try to perform a GWAS of our data, i.e. test each SNP for association with the standing height.
And let's try to do it using linear regression for standing height data
The PLINK option "--bfile /home/student/USER/GWAS/data/European_1w" will specify that the data PLINK should analyse are the files in folder called "/home/student/USER/GWAS/data/" with the prefix "European_1w".
"—linear" specifies that we want to perform GWAS using linear regression
"—adjust" tells PLINK to output a file that includes p-values that are adjusted for multiple testing using Bonferroni correction as well as other fancier methods.
"—autosome" only use autosomes and not X,Y,MT
Now perform the logistic regression on all the SNPs int the dataset using these options in PLINK by typing:
# Start running a GWAS using PLINK2
# running about 3 minutes
source /home/student/miniconda3/bin/activate gwas
plink \
--bfile /home/student/USER/GWAS/data/European_1w \
--linear \
--adjust \
--autosome \
--memory 5000 \
--out ./output/European_1w_standing_height
conda deactivate
(gwas) PLINK v1.90b6.12 64-bit (28 Oct 2019) www.cog-genomics.org/plink/1.9/ (C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to ./output/European_1w_standing_height.log. Options in effect: --adjust --autosome --bfile /home/student/USER/GWAS/data/European_1w --linear --memory 5000 --out ./output/European_1w_standing_height 515181 MB RAM detected; reserving 5000 MB for main workspace. 784256 variants loaded from .bim file. 10000 people (4475 males, 5525 females) loaded from .fam. 10000 phenotype values loaded from .fam. Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 10000 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is 0.970031. 784256 variants and 10000 people pass filters and QC. Phenotype data is quantitative. Writing linear model association results to ./output/European_1w_standing_height.assoc.linear ... done. --adjust: Genomic inflation est. lambda (based on median chisq) = 3.81243. --adjust values (748636 variants) written to ./output/European_1w_standing_height.assoc.linear.adjusted . (gwas)
Take a look at the text PLINK prints to your screen. Specifically, note the
number of SNPs
number of individuals
number of phenotype values
echo "first eight lines"
head ./output/European_1w_standing_height.assoc.linear
echo "significant variants"
awk '$NF<5e-8' ./output/European_1w_standing_height.assoc.linear|head
first eight lines CHR SNP BP A1 TEST NMISS BETA STAT P 1 rs28659788 723307 G ADD 746 0.00252 0.1906 0.8489 1 rs116587930 727841 A ADD 9037 0.01107 3.233 0.001227 1 rs116720794 729632 T ADD 9571 0.001857 0.5359 0.592 1 rs3131972 752721 A ADD 9921 -0.001197 -0.7754 0.4381 1 rs12184325 754105 T ADD 9987 0.001656 0.4847 0.6279 1 rs3131962 756604 A ADD 9978 -0.0007128 -0.4291 0.6678 1 rs114525117 759036 A ADD 9731 0.0005264 0.1498 0.8809 1 rs3115850 761147 T ADD 9494 -5.992e-05 -0.03547 0.9717 1 rs115991721 767096 G ADD 9954 -0.003317 -0.4835 0.6287 significant variants 1 rs57527288 1092563 T ADD 9463 -0.01852 -5.893 3.927e-09 1 rs72631898 1116553 G ADD 9964 -0.01235 -6.817 9.825e-12 1 rs11260563 1165539 A ADD 9984 -0.009136 -6.526 7.079e-11 1 rs6685064 1211292 T ADD 9984 -0.01087 -6.437 1.272e-10 1 rs12751100 1220954 A ADD 9977 -0.01229 -7.262 4.1e-13 1 rs11260578 1221138 A ADD 9922 -0.01527 -6.909 5.176e-12 1 rs1739855 1233941 C ADD 9969 -0.01196 -7.898 3.122e-15 1 rs12142199 1249187 G ADD 9980 -0.009257 -7.258 4.213e-13 1 rs71628956 1301388 G ADD 9988 -0.0102 -6.217 5.285e-10 1 rs141100746 1323143 CCT ADD 9963 -0.009061 -6.883 6.219e-12
Next, plot the results of the GWAS using the following command run in R
# running about 1 minutes
options(repr.plot.width = 16,
repr.plot.height = 4,
repr.plot.res = 600)
source("/home/student/USER/GWAS/data/plotPlink.R")
# plot the results (.assoc.linear is the output file from plink)
plots= plot_qqman(
plink_assoc_file= "./output/European_1w_standing_height.assoc.linear",
pheno_name= "Standing_height",
save_plot = FALSE,
lambda1_qq_pos = c(1.48, -5.5),
lambda2_qq_pos = c(1.1, -4)
)
print(plots$manhattan_plot)
Warning message: “ggrepel: 13666 unlabeled data points (too many overlaps). Consider increasing max.overlaps”
Identify Significance Thresholds¶
Genome-wide significance line – e.g. 5 × 10⁻⁸ for single-variant GWAS or a Bonferroni-corrected line for gene-based tests. Points above it are significant.
Suggestive line (optional) – marks loci worth follow-up but not yet definitive.
A bonferroni corrected p-value threshold based on an initial p-value threshold of 0.05 is not shown on the plot. Explain how this threshold was reached and calculate the exact threshold using your knowledge of how many SNPs you have in your dataset (NB if you want to calculate log10 in R you can use the function log10).
wc -l /home/student/USER/GWAS/data/European_1w.bim
784256 /home/student/USER/GWAS/data/European_1w.bim
from math import log10
print(0.05 / 784_256)
-log10(0.05 / 784_256)
6.375469234535663e-08
7.195487845643804
Using this threshold, does any of the SNPs in your dataset seem to be associated with standing height?
Do your results seem plausible? Why/why not?
awk 'NR>1 && $5 < 6.375469234535663e-08' ./output/European_1w_standing_height.assoc.linear.adjusted | wc -l
awk 'NR>1 && $5 < 5e-08' ./output/European_1w_standing_height.assoc.linear.adjusted | wc -l
2191 2135
Exercise B: checking if it went OK using QQ-plot¶
Now look at the QQ-plot that you already generated (second plot above). Here the red line is the x=y line and the thin curves are a confidence band.
- What does this plot suggest and why?
# running about 0.5 minutes
options(repr.plot.width = 4.1,
repr.plot.height = 4.1,
repr.plot.res = 600)
print(plots$qq_plot)
Axes
X-axis: Expected −log₁₀ P under the null.
Y-axis: Observed −log₁₀ P from your test.
Diagonal (= null)
Points near the diagonal imply well-calibrated statistics.
Genomic inflation factor (λGC)
λ ~ 1 → good; λ ≫ 1 → inflation; λ < 1 → conservative.
Use the QQ-plot together with the Manhattan plot: Manhattan tells where the signals are, QQ-plot tells whether your test statistics are globally trustworthy.
Exercise C: QC your data¶
As you can see, a lot can go wrong if you do not check the quality of your data before running your GWAS! So if you want meaningful/useful output you always have to run a lot of quality checks (QC) before running the association tests. We will try to go through some useful QC steps now.
One potential problem in association studies is spurious relatedness, where some of the individuals in the sample are closely related. Closely related individuals can be inferred with PLINK using the following command, which only uses autosomal SNPs with a minor allele frequency > 5%:
# running about 2 minutes
source /home/student/miniconda3/bin/activate gwas
plink \
--bfile /home/student/USER/GWAS/data/European_1w \
--genome \
--autosome \
--maf 0.05 \
--memory 5000 \
--out ./output/European_1w_genome
conda deactivate
(gwas) PLINK v1.90b6.12 64-bit (28 Oct 2019) www.cog-genomics.org/plink/1.9/ (C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to ./output/European_1w_genome.log. Options in effect: --autosome --bfile /home/student/USER/GWAS/data/European_1w --genome --maf 0.05 --memory 5000 --out ./output/European_1w_genome 515181 MB RAM detected; reserving 5000 MB for main workspace. 784256 variants loaded from .bim file. 10000 people (4475 males, 5525 females) loaded from .fam. 10000 phenotype values loaded from .fam. Using up to 31 threads (change this with --threads). Before main variant filters, 10000 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is 0.970031. 403893 variants removed due to minor allele threshold(s) (--maf/--max-maf/--mac/--max-mac). 380363 variants and 10000 people pass filters and QC. Phenotype data is quantitative. IBD calculations complete. Finished writing ./output/European_1w_genome.genome . (gwas)
head ./output/European_1w_genome.genome
FID1 IID1 FID2 IID2 RT EZ Z0 Z1 Z2 PI_HAT PHE DST PPC RATIO 1000992 1000992 1001118 1001118 UN NA 1.0000 0.0000 0.0000 0.0000 NA 0.740314 0.0000 1.6212 1000992 1000992 1002621 1002621 UN NA 1.0000 0.0000 0.0000 0.0000 NA 0.742542 0.0000 1.7359 1000992 1000992 1002993 1002993 UN NA 1.0000 0.0000 0.0000 0.0000 NA 0.721926 0.0000 1.0538 1000992 1000992 1003258 1003258 UN NA 1.0000 0.0000 0.0000 0.0000 NA 0.741646 0.0000 1.6746 1000992 1000992 1004181 1004181 UN NA 1.0000 0.0000 0.0000 0.0000 NA 0.742432 0.0000 1.6996 1000992 1000992 1004240 1004240 UN NA 1.0000 0.0000 0.0000 0.0000 NA 0.743650 0.0000 1.6686 1000992 1000992 1004285 1004285 UN NA 1.0000 0.0000 0.0000 0.0000 NA 0.741578 0.0000 1.6974 1000992 1000992 1005685 1005685 UN NA 1.0000 0.0000 0.0000 0.0000 NA 0.730170 0.0000 1.3393 1000992 1000992 1006795 1006795 UN NA 1.0000 0.0000 0.0000 0.0000 NA 0.754574 0.0086 1.8577
The results can be summarised in a plot with the following Python code and gives the names of potential related pairs:
# running about 1.5 minutes
import sys
sys.path.append("/home/student/USER/GWAS/data/")
from plotPlink import plot_ibd
plot_ibd("./output/European_1w_genome.genome")
The figure shows estimates of the relatedness for all pairs of individuals.
For each pair k1 is the proportion of the genome where the pair shares 1 of their alleles identical-by-descent (IBD) and k2 is the proportion of the genome where the pair shares both their alleles IBD.
The expected (k1,k2) values for simple relationships are shown in the figure. Are any of the individuals in your dataset closely related?
What assumption in association studies is violated when individuals are related?
And last but not least: how would you recognize if the same person is included twice? (this actually happens often!)
We usually only remove 1. or 2. degree relatives (MZ,PO,FS,HS) from the analysis or we use a mixed model to take the relatedness into account.
Principal component analysis (PCA) and a very similar methods called multidimensional scaling is also often used to reveal problems in the data.
Such analyses can be used to project all the genotype information (e.g. 500,000 marker sites) down to a low number of dimensions e.g. two.
Multidimensional scaling¶
Multidimensional scaling based on your data can be performed with PLINK as follows (the option --mind is used to remove the few individuals which have more than 20% missingness):
# running about 3 minutes
source /home/student/miniconda3/bin/activate gwas
plink \
--bfile /home/student/USER/GWAS/data/European_1w \
--cluster \
--mds-plot 2 \
--mind 0.05 \
--memory 5000 \
--out ./output/European_1w_mds
conda deactivate
PLINK v1.9.0-b.7.8 64-bit (15 Jun 2025) cog-genomics.org/plink/1.9/ (C) 2005-2025 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to ./output/European_1w_mds.log. Options in effect: --bfile /home/student/USER/GWAS/data/European_1w --cluster --mds-plot 2 --memory 5000 --mind 0.05 --out ./output/European_1w_mds 515181 MB RAM detected; reserving 5000 MB for main workspace. 784256 variants loaded from .bim file. 10000 people (4475 males, 5525 females) loaded from .fam. 10000 phenotype values loaded from .fam. 323 people removed due to missing genotype data (--mind). IDs written to ./output/European_1w_mds.irem . Using up to 31 threads (change this with --threads). Before main variant filters, 9677 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate in remaining samples is 0.970822. 784256 variants and 9677 people pass filters and QC. Phenotype data is quantitative. Distance matrix calculation complete. Clustering... done. Cluster solution written to ./output/European_1w_mds.cluster1 , ./output/European_1w_mds.cluster2 , and ./output/European_1w_mds.cluster3 . Performing multidimensional scaling analysis (SVD algorithm, 2 dimensions)... done. MDS solution written to ./output/European_1w_mds.mds .
Try to plot the results in Python:
import sys
sys.path.append("/home/student/USER/GWAS/data/")
from plotPlink import plot_clusters
# plot the results (plink.mds is the output file from plink)
plot_clusters(
"./output/European_1w_mds.mds",
"/home/student/USER/GWAS/data/European_1w.fam"
)
It shows the first two dimensions and each individual is represented by a point.
Clustering of individuals with similar trait values may indicate batch bias or population structure.
- Do you see any clustering or gradients related to the trait values?
- What else could explain such patterns?
Let's perform PCA.
PCA¶
Principal components analysis (PCA) is one of the most useful techniques to visualise genetic diversity in a dataset. The methodology is not restricted to genetic data, but in general allows breaking down high-dimensional datasets to two or more dimensions for visualisation in a two-dimensional space.
Preparing the parameter file¶
For actually running the analysis, we use a software called smartPCA from the Eigensoft package. As many other tools from this and related packages, smartPCA reads in a parameter file which specifies its input and output files and options. The basic format of the parameter file looks like this:
cat /home/student/USER/GWAS/data/European_1w_smartpca.par
genotypename: /home/student/USER/GWAS/data/European_1w.bed snpname: /home/student/USER/GWAS/data/European_1w.bim indivname: /home/student/USER/GWAS/data/European_1w.fam evecoutname: ./output/European_1w.eigenvec evaloutname: ./output/European_1w.eigenval numoutevec: 20 numoutlieriter: 0 numthreads: 30 lsqproject: YES fastmode: NO
Here, the first three parameters specify the input genotype files, as discussed above.
The next two rows specify two output file names, typically with ending *.evec and *.eval.
numoutevec specifies the number of principal components that we compute.
# # do not run!
# # running about 95 minutes
# source /home/student/miniconda3/bin/activate eigensoft
# start_time=$(date +%s)
# smartpca -p \
# /home/student/USER/GWAS/data/European_1w_smartpca.par \
# > ./output/European_1w_pca.log
# end_time=$(date +%s)
# elapsed_seconds=$((end_time - start_time))
# echo "Elapsed time: $(($elapsed_seconds / 60)) mins"
# conda deactivate
Let's examine the pre-run results¶
# check the log
awk 'NR > 16 && NR < 35' /home/student/USER/GWAS/data/European_1w_pca.txt
lsqproject used genetic distance set from physical distance genotype file processed snps deleted (nodata): 0. deletesnpoutname: for detailsnumber of samples used: 10000 number of snps used: 784256 number of pops for axes: 238 Using 29 threads, and partial sum lookup algorithm. snp Affx-89007868 ignored . allelecnt: 0 missing: 9245 snp rs200584816 ignored . allelecnt: 0 missing: 9 snp Affx-80267079 ignored . allelecnt: 0 missing: 9 snp rs200048444 ignored . allelecnt: 0 missing: 8 snp rs144879626 ignored . allelecnt: 0 missing: 127 snp rs139055451 ignored . allelecnt: 0 missing: 117 snp Affx-80290518 ignored . allelecnt: 0 missing: 102 snp Affx-89023000 ignored . allelecnt: 0 missing: 94 snp Affx-80267082 ignored . allelecnt: 0 missing: 23 snp Affx-80210147 ignored . allelecnt: 0 missing: 4 total number of snps killed in pass: 35620 used: 748636 mpstats: 0.768 0.917 1.110 0.372634
# top 10 rows of .eigenvec
head -n 10 /home/student/USER/GWAS/data/European_1w.eigenvec | column -t
# the first line is the eigenvalues for the requested 20 eigenvec
#eigvals: 267.904 85.642 27.427 14.541 8.699 4.969 4.628 4.246 4.017 3.854 3.826 3.709 3.586 3.446 3.308 3.169 3.054 2.875 2.800 2.768 1000992:1000992 -0.0036 0.0213 -0.0248 -0.0101 -0.0042 -0.0044 0.0073 -0.0018 0.0003 -0.0099 -0.0030 0.0045 -0.0000 0.0039 -0.0001 -0.0006 0.0100 0.0049 0.0052 0.0011 1.68 1001118:1001118 0.0031 -0.0034 -0.0012 0.0239 0.0047 0.0013 0.0033 -0.0103 0.0296 0.0034 0.0062 -0.0123 -0.0016 -0.0113 0.0034 0.0115 0.0165 -0.0075 0.0133 0.0009 1.61 1002621:1002621 0.0038 -0.0021 -0.0010 0.0094 -0.0033 -0.0068 0.0060 0.0042 0.0064 -0.0007 0.0129 -0.0125 0.0074 -0.0031 0.0080 -0.0049 -0.0028 -0.0038 -0.0160 -0.0001 1.5 1002993:1002993 -0.0356 -0.0106 0.0007 -0.0007 -0.0039 -0.0091 0.0065 -0.0003 -0.0056 0.0063 -0.0015 -0.0027 -0.0001 0.0084 -0.0031 -0.0100 0.0028 -0.0006 -0.0057 0.0005 1.57 1003258:1003258 0.0045 -0.0039 0.0032 -0.0034 -0.0079 0.0125 0.0251 -0.0113 0.0103 -0.0029 0.0037 0.0053 0.0024 0.0005 -0.0108 -0.0036 -0.0157 -0.0071 -0.0176 -0.0001 1.64 1004181:1004181 0.0042 -0.0030 -0.0002 0.0042 -0.0049 -0.0018 0.0089 -0.0108 0.0002 0.0079 -0.0037 0.0026 -0.0021 0.0052 -0.0039 0.0022 0.0073 -0.0059 0.0051 0.0063 1.76 1004240:1004240 0.0015 0.0004 -0.0092 0.0406 0.0075 0.0027 0.0122 0.0005 -0.0170 0.0066 -0.0171 0.0137 -0.0246 0.0019 -0.0048 0.0050 0.0015 0.0027 0.0090 -0.0148 1.62 1004285:1004285 0.0048 -0.0036 0.0040 -0.0056 -0.0103 0.0144 0.0039 0.0149 -0.0029 -0.0104 0.0087 0.0012 0.0001 -0.0076 -0.0050 0.0016 -0.0112 0.0039 0.0024 0.0032 1.66 1005685:1005685 -0.0287 -0.0095 0.0017 -0.0018 0.0036 -0.0053 0.0010 -0.0022 -0.0025 0.0001 -0.0003 -0.0011 -0.0031 0.0057 -0.0042 0.0007 -0.0025 -0.0068 0.0046 0.0021 1.58
# top 20 rows of .eigenval
head -n 20 /home/student/USER/GWAS/data/European_1w.eigenval
267.904311
85.641806
27.427396
14.540530
8.699140
4.969425
4.628178
4.245519
4.017448
3.853839
3.825826
3.709460
3.585731
3.445973
3.308053
3.168906
3.053775
2.875336
2.800393
2.768408
Let's visualize the results of PCA.
# running about 0.5 minutes
import sys
sys.path.append("/home/student/USER/GWAS/data/")
from plotPCA import plot_pca_plots
plot_pca_plots(
eigenvec_file="/home/student/USER/GWAS/data/European_1w_fig.eigenvec",
country_file="/home/student/USER/GWAS/data/European_1w_phenotypes.txt",
save_figs=False
)
Done.
It shows the first several PCs capture very strong population structure.
The dataset exhibits pronounced population structure.
These PCs can be safely used as covariates in downstream GWAS.
Tracy-Widom statistics¶
The twstats program computes Tracy-Widom statistics to evaluate the statistical significance of each principal component identified by pca.
# the head 8 rows of Tracy-Widom statistics
awk 'NR > 35 && NR < 46' /home/student/USER/GWAS/data/European_1w_pca.txt
## Tracy-Widom statistics: rows: 10000 cols: 784256 #N eigenvalue difference twstat p-value effect. n 1 267.904311 NA 6935.282 0 1249.238 2 85.641806 -182.262506 16467.926 0 10758.264 3 27.427396 -58.214410 18345.254 0 56938.226 4 14.540530 -12.886866 13526.745 0 99068.447 5 8.699140 -5.841389 8627.566 0 123066.090 6 4.969425 -3.729715 4365.905 0 133510.288 7 4.628178 -0.341247 3998.900 0 136555.209 8 4.245519 -0.382659 3555.823 0 139204.953
awk 'NR >= 38 && NR <= 10036 && $5 != "NA" && ($5+0) < 0.05' /home/student/USER/GWAS/data/European_1w_pca.txt | wc -l
676
Among the top 676 principal components (PCs) that showed statistical significance, we retained only the top 20 PCs for downstream analyses as an illustrative example."
head /home/student/USER/GWAS/data/covar_PCs.txt | column -t
FID IID PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 PC14 PC15 PC16 PC17 PC18 PC19 PC20 1000992 1000992 -0.0036 0.0213 -0.0248 -0.0101 -0.0042 -0.0044 0.0073 -0.0018 0.0003 -0.0099 -0.0030 0.0045 -0.0000 0.0039 -0.0001 -0.0006 0.0100 0.0049 0.0052 0.0011 1001118 1001118 0.0031 -0.0034 -0.0012 0.0239 0.0047 0.0013 0.0033 -0.0103 0.0296 0.0034 0.0062 -0.0123 -0.0016 -0.0113 0.0034 0.0115 0.0165 -0.0075 0.0133 0.0009 1002621 1002621 0.0038 -0.0021 -0.0010 0.0094 -0.0033 -0.0068 0.0060 0.0042 0.0064 -0.0007 0.0129 -0.0125 0.0074 -0.0031 0.0080 -0.0049 -0.0028 -0.0038 -0.0160 -0.0001 1002993 1002993 -0.0356 -0.0106 0.0007 -0.0007 -0.0039 -0.0091 0.0065 -0.0003 -0.0056 0.0063 -0.0015 -0.0027 -0.0001 0.0084 -0.0031 -0.0100 0.0028 -0.0006 -0.0057 0.0005 1003258 1003258 0.0045 -0.0039 0.0032 -0.0034 -0.0079 0.0125 0.0251 -0.0113 0.0103 -0.0029 0.0037 0.0053 0.0024 0.0005 -0.0108 -0.0036 -0.0157 -0.0071 -0.0176 -0.0001 1004181 1004181 0.0042 -0.0030 -0.0002 0.0042 -0.0049 -0.0018 0.0089 -0.0108 0.0002 0.0079 -0.0037 0.0026 -0.0021 0.0052 -0.0039 0.0022 0.0073 -0.0059 0.0051 0.0063 1004240 1004240 0.0015 0.0004 -0.0092 0.0406 0.0075 0.0027 0.0122 0.0005 -0.0170 0.0066 -0.0171 0.0137 -0.0246 0.0019 -0.0048 0.0050 0.0015 0.0027 0.0090 -0.0148 1004285 1004285 0.0048 -0.0036 0.0040 -0.0056 -0.0103 0.0144 0.0039 0.0149 -0.0029 -0.0104 0.0087 0.0012 0.0001 -0.0076 -0.0050 0.0016 -0.0112 0.0039 0.0024 0.0032 1005685 1005685 -0.0287 -0.0095 0.0017 -0.0018 0.0036 -0.0053 0.0010 -0.0022 -0.0025 0.0001 -0.0003 -0.0011 -0.0031 0.0057 -0.0042 0.0007 -0.0025 -0.0068 0.0046 0.0021
Adiitionally, let's try to fix the issue by filtering SNPs. We can remove many of the error prone SNPs by removing
SNPs that are not in HWE (Hardy weinberg Equilibrium) (option --hwe)
the rare SNPs (difficult to genotype and very error prone) (option --maf)
SNPs with lots of missing data (why?) (option --geno)
Try to redo the above plink analysis by adding the additional filters
--hwe 0.0001 --maf 0.05 --geno 0.05
which remove sites not in HWE (p-value 0.0001), low minor allele frequency (<5%), high genotype missingness (>5%).
- Can you now see patterns or gradients among individuals with respect to the quantitative trait?
Let us try to rerun an association analysis with these additional filters (and a new output name so we won't overwrite our old results).
# # do not run!
# # running about 4 hours
# source /home/student/miniconda3/bin/activate gwas
# plink \
# --bfile /home/student/USER/GWAS/data/European_1w \
# --linear hide-covar \
# --autosome \
# --memory 5000 \
# --out ./output/European_1w_QC_PC20 \
# --hwe 0.0001 \
# --maf 0.05 \
# --geno 0.05 \
# --covar /home/student/USER/GWAS/data/covar_PCs.txt \
# --covar-name PC1-PC20
# conda deactivate
(gwas) PLINK v1.90b6.12 64-bit (28 Oct 2019) www.cog-genomics.org/plink/1.9/ (C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to ./output/European_1w_QC_PC20.log. Options in effect: --autosome --bfile /home/student/USER/GWAS/data/European_1w --covar /home/student/USER/GWAS/data/covar_PCs.txt --covar-name PC1-PC20 --geno 0.05 --hwe 0.0001 --linear hide-covar --maf 0.05 --memory 5000 --out ./output/European_1w_QC_PC20 515181 MB RAM detected; reserving 5000 MB for main workspace. 784256 variants loaded from .bim file. 10000 people (4475 males, 5525 females) loaded from .fam. 10000 phenotype values loaded from .fam. Using 1 thread (no multithreaded calculations invoked). --covar: 20 covariates loaded. Before main variant filters, 10000 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is 0.970031. 70335 variants removed due to missing genotype data (--geno). --hwe: 99409 variants removed due to Hardy-Weinberg exact test. 337247 variants removed due to minor allele threshold(s) (--maf/--max-maf/--mac/--max-mac). 277265 variants and 10000 people pass filters and QC. Phenotype data is quantitative. Writing linear model association results to ./output/European_1w_QC_PC20.assoc.linear ... done. (gwas)
Now try to plot the manhattan plot and the qqplot in R:
# running about 1 minutes
options(repr.plot.width = 16,
repr.plot.height = 4,
repr.plot.res = 600)
source("/home/student/USER/GWAS/data/plotPlink.R")
# plot the results (.assoc.linear is the output file from plink)
plots= plot_qqman(
plink_assoc_file= "/home/student/USER/GWAS/data/European_1w_QC_PC20.assoc.linear",
pheno_name= "Standing_height",
save_plot = FALSE,
lambda1_qq_pos = c(1.48, -5.5),
lambda2_qq_pos = c(1.1, -4)
)
print(plots$manhattan_plot)
# running about 0.5 minutes
options(repr.plot.width = 4.1,
repr.plot.height = 4.1,
repr.plot.res = 600)
print(plots$qq_plot)
- How does the QQ plot look now - any signs of inflation?
- How many genome wide significant SNPs?
Information about the most significant SNPs is printed below.
Identify the chromosome, physical position (BP), beta and SNP name.
head /home/student/USER/GWAS/data/European_1w_QC_PC20.assoc.linear
awk 'NR>1 {print $1,$2,$3,$9}' \
/home/student/USER/GWAS/data/European_1w_QC_PC20.assoc.linear | sort -k4,4g 2>/dev/null | head -1 || true
CHR SNP BP A1 TEST NMISS BETA STAT P 1 rs57181708 809876 G ADD 9990 0.000702 0.3443 0.7306 1 rs4422948 835499 G ADD 9803 0.0003526 0.2356 0.8138 1 rs4970383 838555 A ADD 9974 4.12e-05 0.02801 0.9777 1 rs4970382 840753 C ADD 9970 0.001852 1.414 0.1575 1 rs950122 846864 C ADD 9928 0.0001695 0.1042 0.917 1 rs13303222 849998 A ADD 9963 -0.0009964 -0.5865 0.5576 1 rs6657440 850780 C ADD 9980 -0.0004311 -0.324 0.746 1 rs4970459 858051 T ADD 9979 0.001015 0.62 0.5352 1 rs74047407 866938 A ADD 9987 0.00195 1.27 0.2042 7 rs7808919 7902687 7.02e-07
Let's try to plot the region with the most significant SNP in a 1 Mb window around this SNP:
awk '{$1=$1}1' OFS='\t' /home/student/USER/GWAS/data/European_1w_QC_PC20.assoc.linear > ./output/European_1w_QC_PC20.assoc_linear.txt
source /home/student/miniconda3/bin/activate py2
/home/student/USER/GWAS/locuszoom/bin/locuszoom \
--metal ./output/European_1w_QC_PC20.assoc_linear.txt \
--markercol SNP \
--pvalcol P \
--refsnp rs7808919 \
--chr 7 \
--flank 500kb \
--pop EUR \
--build hg19 \
--source 1000G_March2012 \
--prefix ./output/European_1w
conda deactivate
(py2) +-------------------------------------------+ | LocusZoom 1.4 (05/01/2017) | | Plot regional association results | | from GWA scans or candidate gene studies | +-------------------------------------------+ Loading settings.. Options in effect are: +------------+--------------------------------------+ | Option | Value | +------------+--------------------------------------+ | metal | European_1w_QC_PC20.assoc_linear.txt | | markercol | SNP | | pvalcol | P | | refsnp | rs7808919 | | flank | 500000 | | build | hg19 | | ld-measure | rsquare | | pop | EUR | | source | 1000G_March2012 | | snpset | Illu1M | | gene-table | refFlat | | cache | ../ld_cache.db | +------------+--------------------------------------+ Using /home/student/USER/GWAS/locuszoom/bin/locuszoom.R.. Beginning plotting sequence for: rs7808919 Extracting region of interest (chr7:7402687-8402687) from input file.. Finding pairwise LD with reference SNP rs7808919.. Source: 1000G_March2012 | Population: EUR | Build: hg19 Using /home/student/miniconda3/envs/py2/bin/plink to compute LD.. Warning: could not locate LD cache database, tried: ../ld_cache.db, creating new one.. Grabbing annotations from SQLite database.. Creating plot.. 警告信息: 程序包‘lattice’是用R版本4.4.3 来建造的 Read 11 items Deleting temporary files.. Time required: 0d:0h:0m:2s (py2)
Open the figure manually using this path:
./output/European_1w_250716_rs7808919/chr7_7402687-8402687.pdf
Step0: Format the data as needed¶
head /home/student/USER/GWAS/data/phenotype.txt
FID IID phenotype 3914956 3914956 1.75 3713468 3713468 1.56 5771003 5771003 1.59 5288656 5288656 1.71 4557604 4557604 1.41 3756910 3756910 1.48 1770301 1770301 1.66 2325183 2325183 1.625 1495340 1495340 1.94
Part 1: perform regenie analyses without considering the top 20 pcs¶
Step1: fitting the null linear mixed model with regenie¶
For quantitative traits (such as standing height), regenie fits a linear mixed model by default.
It is recommended to inverse normalize the phenotype before analysis to improve normality and statistical power.
# running about 2 minutes
source /home/student/miniconda3/bin/activate regenie_env
regenie \
--step 1 \
--bed /home/student/USER/GWAS/data/European_1w_QC \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--loocv \
--lowmem \
--lowmem-prefix ./output/regenie_tmp_preds \
--apply-rint \
--out ./output/regenie_step1_WO_PC20
conda deactivate
(regenie_env) Start time: Sat Jul 19 14:42:15 2025
|===========================|
| REGENIE v4.1.gz |
|===========================|
Copyright (c) 2020-2024 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.
Compiled with Boost Iostream library.
Using Intel MKL with Eigen.
Log of output saved in file : ./output/regenie_step1_WO_PC20.log
Options in effect:
--step 1 \
--bed /home/student/USER/GWAS/data/European_1w_QC \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--loocv \
--lowmem \
--lowmem-prefix ./output/regenie_tmp_preds \
--apply-rint \
--out ./output/regenie_step1_WO_PC20
Fitting null model
* bim : [/home/student/USER/GWAS/data/European_1w_QC.bim] n_snps = 277265
* fam : [/home/student/USER/GWAS/data/European_1w_QC.fam] n_samples = 10000
* bed : [/home/student/USER/GWAS/data/European_1w_QC.bed]
* phenotypes : [/home/student/USER/GWAS/data/phenotype.txt] n_pheno = 1
-dropping observations with missing values at any of the phenotypes
-number of phenotyped individuals with no missing data = 10000
* number of individuals used in analysis = 10000
-applying RINT to all phenotypes
* number of observations for each trait:
- 'phenotype': 10000 observations
-residualizing and scaling phenotypes...done (0ms)
* # threads : [31]
* block size : [1000]
* # blocks : [288] for 277265 variants
* # CV folds : [10000]
* ridge data_l0 : [ 5 : 0.01 0.25 0.5 0.75 0.99 ]
* ridge data_l1 : [ 5 : 0.01 0.25 0.5 0.75 0.99 ]
* approximate memory usage : 2GB
* writing level 0 predictions to disk
-temporary files will have prefix [./output/regenie_tmp_preds_l0_Y]
-approximate disk space needed : 110MB
* setting memory...done
Chromosome 1
block [1] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (70ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (83ms)
block [2] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [3] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (82ms)
block [4] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [5] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (84ms)
block [6] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (84ms)
block [7] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [8] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (83ms)
block [9] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [10] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (57ms)
-calc working matrices...done (146ms)
-calc level 0 ridge...done (82ms)
block [11] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [12] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [13] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (81ms)
block [14] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (82ms)
block [15] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (81ms)
block [16] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (81ms)
block [17] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [18] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (81ms)
block [19] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (80ms)
block [20] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [21] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (84ms)
block [22] : 569 snps (6ms)
-residualizing and scaling genotypes...done (33ms)
-calc working matrices...done (53ms)
-calc level 0 ridge...done (43ms)
Chromosome 2
block [23] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (81ms)
block [24] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [25] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [26] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (82ms)
block [27] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [28] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (82ms)
block [29] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (82ms)
block [30] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (137ms)
-calc level 0 ridge...done (83ms)
block [31] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [32] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (83ms)
block [33] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (85ms)
block [34] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (81ms)
block [35] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (81ms)
block [36] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (81ms)
block [37] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (81ms)
block [38] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [39] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (82ms)
block [40] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [41] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [42] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (82ms)
block [43] : 836 snps (13ms)
-residualizing and scaling genotypes...done (47ms)
-calc working matrices...done (105ms)
-calc level 0 ridge...done (67ms)
Chromosome 3
block [44] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (81ms)
block [45] : 1000 snps (24ms)
-residualizing and scaling genotypes...done (54ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [46] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (82ms)
block [47] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [48] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [49] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (82ms)
block [50] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [51] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (83ms)
block [52] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [53] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [54] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (94ms)
block [55] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [56] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [57] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (84ms)
block [58] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (247ms)
-calc level 0 ridge...done (83ms)
block [59] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (82ms)
block [60] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (83ms)
block [61] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [62] : 271 snps (3ms)
-residualizing and scaling genotypes...done (15ms)
-calc working matrices...done (13ms)
-calc level 0 ridge...done (21ms)
Chromosome 4
block [63] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (88ms)
block [64] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (150ms)
-calc level 0 ridge...done (83ms)
block [65] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (163ms)
-calc level 0 ridge...done (81ms)
block [66] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (138ms)
-calc level 0 ridge...done (82ms)
block [67] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (85ms)
block [68] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [69] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [70] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [71] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (82ms)
block [72] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (82ms)
block [73] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (82ms)
block [74] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [75] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [76] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (82ms)
block [77] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (140ms)
-calc level 0 ridge...done (83ms)
block [78] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [79] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [80] : 115 snps (1ms)
-residualizing and scaling genotypes...done (9ms)
-calc working matrices...done (20ms)
-calc level 0 ridge...done (21ms)
Chromosome 5
block [81] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (150ms)
-calc level 0 ridge...done (83ms)
block [82] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (67ms)
-calc working matrices...done (147ms)
-calc level 0 ridge...done (81ms)
block [83] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (400ms)
-calc level 0 ridge...done (82ms)
block [84] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (120ms)
-calc level 0 ridge...done (82ms)
block [85] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (119ms)
-calc level 0 ridge...done (82ms)
block [86] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (82ms)
block [87] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (118ms)
-calc level 0 ridge...done (82ms)
block [88] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (82ms)
block [89] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (116ms)
-calc level 0 ridge...done (81ms)
block [90] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (120ms)
-calc level 0 ridge...done (83ms)
block [91] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [92] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (67ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (81ms)
block [93] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (144ms)
-calc level 0 ridge...done (82ms)
block [94] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (67ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (83ms)
block [95] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (81ms)
block [96] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [97] : 416 snps (9ms)
-residualizing and scaling genotypes...done (29ms)
-calc working matrices...done (29ms)
-calc level 0 ridge...done (27ms)
Chromosome 6
block [98] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [99] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (84ms)
block [100] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (81ms)
block [101] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (57ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [102] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [103] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (113ms)
-calc level 0 ridge...done (80ms)
block [104] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (112ms)
-calc level 0 ridge...done (81ms)
block [105] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (88ms)
block [106] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (113ms)
-calc level 0 ridge...done (81ms)
block [107] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (82ms)
block [108] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (57ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [109] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (148ms)
-calc level 0 ridge...done (82ms)
block [110] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [111] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (82ms)
block [112] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (82ms)
block [113] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (82ms)
block [114] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (81ms)
block [115] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (82ms)
block [116] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [117] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [118] : 373 snps (4ms)
-residualizing and scaling genotypes...done (21ms)
-calc working matrices...done (27ms)
-calc level 0 ridge...done (24ms)
Chromosome 7
block [119] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (137ms)
-calc level 0 ridge...done (82ms)
block [120] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [121] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [122] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (81ms)
block [123] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [124] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [125] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [126] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (81ms)
block [127] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [128] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (81ms)
block [129] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (83ms)
block [130] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (74ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (85ms)
block [131] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (68ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (85ms)
block [132] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (143ms)
-calc level 0 ridge...done (82ms)
block [133] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (138ms)
-calc level 0 ridge...done (82ms)
block [134] : 265 snps (3ms)
-residualizing and scaling genotypes...done (17ms)
-calc working matrices...done (20ms)
-calc level 0 ridge...done (18ms)
Chromosome 8
block [135] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (84ms)
block [136] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (85ms)
block [137] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (84ms)
block [138] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (84ms)
block [139] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (85ms)
block [140] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (85ms)
block [141] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (85ms)
block [142] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (85ms)
block [143] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (85ms)
block [144] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (88ms)
block [145] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (85ms)
block [146] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (86ms)
block [147] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (88ms)
block [148] : 906 snps (12ms)
-residualizing and scaling genotypes...done (54ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (74ms)
Chromosome 9
block [149] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (84ms)
block [150] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (84ms)
block [151] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (83ms)
block [152] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (153ms)
-calc level 0 ridge...done (85ms)
block [153] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (85ms)
block [154] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (84ms)
block [155] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (84ms)
block [156] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (294ms)
-calc level 0 ridge...done (85ms)
block [157] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (85ms)
block [158] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (85ms)
block [159] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (86ms)
block [160] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (57ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (85ms)
block [161] : 564 snps (9ms)
-residualizing and scaling genotypes...done (31ms)
-calc working matrices...done (56ms)
-calc level 0 ridge...done (42ms)
Chromosome 10
block [162] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (82ms)
block [163] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [164] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [165] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (83ms)
block [166] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (82ms)
block [167] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (82ms)
block [168] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (143ms)
-calc level 0 ridge...done (81ms)
block [169] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (287ms)
-calc level 0 ridge...done (82ms)
block [170] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (82ms)
block [171] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [172] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (82ms)
block [173] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (82ms)
block [174] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (83ms)
block [175] : 692 snps (11ms)
-residualizing and scaling genotypes...done (39ms)
-calc working matrices...done (66ms)
-calc level 0 ridge...done (52ms)
Chromosome 11
block [176] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [177] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (81ms)
block [178] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (54ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (81ms)
block [179] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (138ms)
-calc level 0 ridge...done (82ms)
block [180] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (81ms)
block [181] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (81ms)
block [182] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (82ms)
block [183] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (81ms)
block [184] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [185] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [186] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [187] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (80ms)
block [188] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [189] : 711 snps (7ms)
-residualizing and scaling genotypes...done (42ms)
-calc working matrices...done (78ms)
-calc level 0 ridge...done (56ms)
Chromosome 12
block [190] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (82ms)
block [191] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [192] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (143ms)
-calc level 0 ridge...done (83ms)
block [193] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [194] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [195] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [196] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [197] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (81ms)
block [198] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (179ms)
-calc level 0 ridge...done (84ms)
block [199] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (144ms)
-calc level 0 ridge...done (83ms)
block [200] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (81ms)
block [201] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (81ms)
block [202] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (140ms)
-calc level 0 ridge...done (81ms)
block [203] : 453 snps (4ms)
-residualizing and scaling genotypes...done (27ms)
-calc working matrices...done (35ms)
-calc level 0 ridge...done (34ms)
Chromosome 13
block [204] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (81ms)
block [205] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (80ms)
block [206] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (80ms)
block [207] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (82ms)
block [208] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [209] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (80ms)
block [210] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [211] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (80ms)
block [212] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (80ms)
block [213] : 597 snps (6ms)
-residualizing and scaling genotypes...done (36ms)
-calc working matrices...done (59ms)
-calc level 0 ridge...done (46ms)
Chromosome 14
block [214] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [215] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [216] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (161ms)
-calc level 0 ridge...done (82ms)
block [217] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (81ms)
block [218] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [219] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (82ms)
block [220] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (152ms)
-calc level 0 ridge...done (82ms)
block [221] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [222] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [223] : 1 snps (0ms)
-residualizing and scaling genotypes...done (0ms)
-calc working matrices...done (0ms)
-calc level 0 ridge...done (2ms)
Chromosome 15
block [224] : 1000 snps (28ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (82ms)
block [225] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (81ms)
block [226] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [227] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (54ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (81ms)
block [228] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (54ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (82ms)
block [229] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (54ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [230] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [231] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (54ms)
-calc working matrices...done (143ms)
-calc level 0 ridge...done (81ms)
block [232] : 680 snps (15ms)
-residualizing and scaling genotypes...done (37ms)
-calc working matrices...done (75ms)
-calc level 0 ridge...done (55ms)
Chromosome 16
block [233] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [234] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [235] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [236] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [237] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [238] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [239] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [240] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [241] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [242] : 907 snps (10ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (81ms)
Chromosome 17
block [243] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (82ms)
block [244] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [245] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [246] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [247] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [248] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [249] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [250] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [251] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (82ms)
block [252] : 357 snps (4ms)
-residualizing and scaling genotypes...done (20ms)
-calc working matrices...done (24ms)
-calc level 0 ridge...done (23ms)
Chromosome 18
block [253] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [254] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [255] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [256] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [257] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [258] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [259] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [260] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [261] : 521 snps (5ms)
-residualizing and scaling genotypes...done (30ms)
-calc working matrices...done (40ms)
-calc level 0 ridge...done (38ms)
Chromosome 19
block [262] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [263] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [264] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (81ms)
block [265] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (83ms)
block [266] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [267] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (82ms)
block [268] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (81ms)
block [269] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (81ms)
block [270] : 363 snps (4ms)
-residualizing and scaling genotypes...done (21ms)
-calc working matrices...done (29ms)
-calc level 0 ridge...done (25ms)
Chromosome 20
block [271] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (141ms)
-calc level 0 ridge...done (83ms)
block [272] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (82ms)
block [273] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [274] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (81ms)
block [275] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [276] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (57ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (84ms)
block [277] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (83ms)
block [278] : 369 snps (4ms)
-residualizing and scaling genotypes...done (20ms)
-calc working matrices...done (28ms)
-calc level 0 ridge...done (23ms)
Chromosome 21
block [279] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [280] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (55ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (81ms)
block [281] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [282] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [283] : 379 snps (4ms)
-residualizing and scaling genotypes...done (22ms)
-calc working matrices...done (25ms)
-calc level 0 ridge...done (24ms)
Chromosome 22
block [284] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (82ms)
block [285] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (84ms)
block [286] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (57ms)
-calc working matrices...done (146ms)
-calc level 0 ridge...done (81ms)
block [287] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (56ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [288] : 920 snps (20ms)
-residualizing and scaling genotypes...done (50ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (78ms)
Level 1 ridge...
-on phenotype 1 (phenotype)...done (363ms)
Output
------
phenotype 1 (phenotype) :
0.01 : Rsq = 0.0407994, MSE = 0.959384
0.25 : Rsq = 0.0489394, MSE = 0.953553<- min value
0.5 : Rsq = 0.0477102, MSE = 0.961199
0.75 : Rsq = 0.0475974, MSE = 0.967915
0.99 : Rsq = 0.0493501, MSE = 0.984369
* making predictions...writing LOCO predictions...done (533ms)
List of blup files written to: [./output/regenie_step1_WO_PC20_pred.list]
Elapsed time : 84.914s
End time: Sat Jul 19 14:43:40 2025
(regenie_env)
See more parameter explanations: https://rgcgithub.github.io/regenie/options/.
Step 2: performing single-variant association tests¶
For quantitative traits (such as standing height), regenie automatically uses a linear mixed model for association testing.
There is no need for saddle point approximation or Firth correction, as these are specific to binary traits.
The output will include effect sizes, standard errors, and p-values for each variant.
# running about 0.5 minutes
source /home/student/miniconda3/bin/activate regenie_env
regenie \
--step 2 \
--bed /home/student/USER/GWAS/data/European_1w_QC \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_WO_PC20_pred.list \
--out ./output/regenie_step2_asso_WO_PC20
conda deactivate
(regenie_env) Start time: Tue Jul 22 22:02:47 2025
|===========================|
| REGENIE v4.1.gz |
|===========================|
Copyright (c) 2020-2024 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.
Compiled with Boost Iostream library.
Using Intel MKL with Eigen.
Log of output saved in file : ./output/regenie_step2_asso_WO_PC20.log
Options in effect:
--step 2 \
--bed /home/student/USER/GWAS/data/European_1w_QC \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_WO_PC20_pred.list \
--out ./output/regenie_step2_asso_WO_PC20
Association testing mode with fast multithreading using OpenMP
* bim : [/home/student/USER/GWAS/data/European_1w_QC.bim] n_snps = 277265
* fam : [/home/student/USER/GWAS/data/European_1w_QC.fam] n_samples = 10000
* bed : [/home/student/USER/GWAS/data/European_1w_QC.bed]
* phenotypes : [/home/student/USER/GWAS/data/phenotype.txt] n_pheno = 1
-dropping observations with missing values at any of the phenotypes
-number of phenotyped individuals with no missing data = 10000
* number of individuals used in analysis = 10000
-applying RINT to all phenotypes
* number of observations for each trait:
- 'phenotype': 10000 observations
* LOCO predictions : [./output/regenie_step1_WO_PC20_pred.list]
-file [/home/tch_lz/./output/regenie_step1_WO_PC20_1.loco] for phenotype 'phenotype'
+ 9955 individuals with missing LOCO predictions will be ignored for the trait
-residualizing and scaling phenotypes...done (0ms)
* # threads : [31]
* block size : [1000]
* # blocks : [288]
* approximate memory usage : 228MB
* using minimum MAC of 5 (variants with lower MAC are ignored)
Chromosome 1 [22 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [1/288] : done (11ms)
block [2/288] : done (4ms)
block [3/288] : done (4ms)
block [4/288] : done (4ms)
block [5/288] : done (8ms)
block [6/288] : done (11ms)
block [7/288] : done (11ms)
block [8/288] : done (11ms)
block [9/288] : done (11ms)
block [10/288] : done (15ms)
block [11/288] : done (8ms)
block [12/288] : done (4ms)
block [13/288] : done (4ms)
block [14/288] : done (4ms)
block [15/288] : done (4ms)
block [16/288] : done (4ms)
block [17/288] : done (4ms)
block [18/288] : done (4ms)
block [19/288] : done (4ms)
block [20/288] : done (4ms)
block [21/288] : done (4ms)
block [22/288] : done (5ms)
Chromosome 2 [21 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [23/288] : done (8ms)
block [24/288] : done (4ms)
block [25/288] : done (4ms)
block [26/288] : done (4ms)
block [27/288] : done (4ms)
block [28/288] : done (4ms)
block [29/288] : done (4ms)
block [30/288] : done (4ms)
block [31/288] : done (4ms)
block [32/288] : done (4ms)
block [33/288] : done (4ms)
block [34/288] : done (4ms)
block [35/288] : done (4ms)
block [36/288] : done (4ms)
block [37/288] : done (4ms)
block [38/288] : done (4ms)
block [39/288] : done (4ms)
block [40/288] : done (4ms)
block [41/288] : done (4ms)
block [42/288] : done (4ms)
block [43/288] : done (8ms)
Chromosome 3 [19 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [44/288] : done (9ms)
block [45/288] : done (4ms)
block [46/288] : done (4ms)
block [47/288] : done (4ms)
block [48/288] : done (4ms)
block [49/288] : done (4ms)
block [50/288] : done (4ms)
block [51/288] : done (4ms)
block [52/288] : done (4ms)
block [53/288] : done (4ms)
block [54/288] : done (4ms)
block [55/288] : done (4ms)
block [56/288] : done (4ms)
block [57/288] : done (4ms)
block [58/288] : done (4ms)
block [59/288] : done (4ms)
block [60/288] : done (11ms)
block [61/288] : done (4ms)
block [62/288] : done (3ms)
Chromosome 4 [18 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [63/288] : done (9ms)
block [64/288] : done (5ms)
block [65/288] : done (4ms)
block [66/288] : done (4ms)
block [67/288] : done (4ms)
block [68/288] : done (4ms)
block [69/288] : done (4ms)
block [70/288] : done (4ms)
block [71/288] : done (4ms)
block [72/288] : done (4ms)
block [73/288] : done (4ms)
block [74/288] : done (4ms)
block [75/288] : done (4ms)
block [76/288] : done (4ms)
block [77/288] : done (4ms)
block [78/288] : done (4ms)
block [79/288] : done (4ms)
block [80/288] : done (0ms)
Chromosome 5 [17 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [81/288] : done (8ms)
block [82/288] : done (4ms)
block [83/288] : done (4ms)
block [84/288] : done (4ms)
block [85/288] : done (4ms)
block [86/288] : done (4ms)
block [87/288] : done (4ms)
block [88/288] : done (4ms)
block [89/288] : done (4ms)
block [90/288] : done (4ms)
block [91/288] : done (4ms)
block [92/288] : done (4ms)
block [93/288] : done (4ms)
block [94/288] : done (4ms)
block [95/288] : done (4ms)
block [96/288] : done (4ms)
block [97/288] : done (4ms)
Chromosome 6 [21 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [98/288] : done (9ms)
block [99/288] : done (4ms)
block [100/288] : done (4ms)
block [101/288] : done (4ms)
block [102/288] : done (4ms)
block [103/288] : done (4ms)
block [104/288] : done (4ms)
block [105/288] : done (4ms)
block [106/288] : done (4ms)
block [107/288] : done (7ms)
block [108/288] : done (4ms)
block [109/288] : done (4ms)
block [110/288] : done (8ms)
block [111/288] : done (11ms)
block [112/288] : done (11ms)
block [113/288] : done (11ms)
block [114/288] : done (6ms)
block [115/288] : done (4ms)
block [116/288] : done (4ms)
block [117/288] : done (8ms)
block [118/288] : done (9ms)
Chromosome 7 [16 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [119/288] : done (8ms)
block [120/288] : done (8ms)
block [121/288] : done (11ms)
block [122/288] : done (11ms)
block [123/288] : done (11ms)
block [124/288] : done (11ms)
block [125/288] : done (6ms)
block [126/288] : done (4ms)
block [127/288] : done (4ms)
block [128/288] : done (4ms)
block [129/288] : done (4ms)
block [130/288] : done (4ms)
block [131/288] : done (4ms)
block [132/288] : done (4ms)
block [133/288] : done (4ms)
block [134/288] : done (1ms)
Chromosome 8 [14 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [135/288] : done (9ms)
block [136/288] : done (4ms)
block [137/288] : done (4ms)
block [138/288] : done (4ms)
block [139/288] : done (4ms)
block [140/288] : done (4ms)
block [141/288] : done (4ms)
block [142/288] : done (4ms)
block [143/288] : done (4ms)
block [144/288] : done (4ms)
block [145/288] : done (4ms)
block [146/288] : done (4ms)
block [147/288] : done (4ms)
block [148/288] : done (8ms)
Chromosome 9 [13 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [149/288] : done (9ms)
block [150/288] : done (4ms)
block [151/288] : done (4ms)
block [152/288] : done (4ms)
block [153/288] : done (4ms)
block [154/288] : done (4ms)
block [155/288] : done (4ms)
block [156/288] : done (4ms)
block [157/288] : done (4ms)
block [158/288] : done (4ms)
block [159/288] : done (4ms)
block [160/288] : done (4ms)
block [161/288] : done (5ms)
Chromosome 10 [14 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [162/288] : done (9ms)
block [163/288] : done (5ms)
block [164/288] : done (4ms)
block [165/288] : done (4ms)
block [166/288] : done (4ms)
block [167/288] : done (4ms)
block [168/288] : done (4ms)
block [169/288] : done (4ms)
block [170/288] : done (4ms)
block [171/288] : done (4ms)
block [172/288] : done (4ms)
block [173/288] : done (4ms)
block [174/288] : done (4ms)
block [175/288] : done (6ms)
Chromosome 11 [14 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [176/288] : done (9ms)
block [177/288] : done (4ms)
block [178/288] : done (4ms)
block [179/288] : done (4ms)
block [180/288] : done (4ms)
block [181/288] : done (4ms)
block [182/288] : done (4ms)
block [183/288] : done (5ms)
block [184/288] : done (5ms)
block [185/288] : done (4ms)
block [186/288] : done (4ms)
block [187/288] : done (4ms)
block [188/288] : done (4ms)
block [189/288] : done (6ms)
Chromosome 12 [14 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [190/288] : done (9ms)
block [191/288] : done (4ms)
block [192/288] : done (4ms)
block [193/288] : done (4ms)
block [194/288] : done (4ms)
block [195/288] : done (4ms)
block [196/288] : done (4ms)
block [197/288] : done (4ms)
block [198/288] : done (4ms)
block [199/288] : done (4ms)
block [200/288] : done (4ms)
block [201/288] : done (4ms)
block [202/288] : done (4ms)
block [203/288] : done (4ms)
Chromosome 13 [10 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [204/288] : done (8ms)
block [205/288] : done (4ms)
block [206/288] : done (6ms)
block [207/288] : done (4ms)
block [208/288] : done (4ms)
block [209/288] : done (4ms)
block [210/288] : done (4ms)
block [211/288] : done (4ms)
block [212/288] : done (4ms)
block [213/288] : done (5ms)
Chromosome 14 [10 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [214/288] : done (8ms)
block [215/288] : done (4ms)
block [216/288] : done (4ms)
block [217/288] : done (4ms)
block [218/288] : done (4ms)
block [219/288] : done (4ms)
block [220/288] : done (4ms)
block [221/288] : done (4ms)
block [222/288] : done (4ms)
block [223/288] : done (0ms)
Chromosome 15 [9 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [224/288] : done (9ms)
block [225/288] : done (4ms)
block [226/288] : done (4ms)
block [227/288] : done (4ms)
block [228/288] : done (4ms)
block [229/288] : done (4ms)
block [230/288] : done (4ms)
block [231/288] : done (4ms)
block [232/288] : done (6ms)
Chromosome 16 [10 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [233/288] : done (9ms)
block [234/288] : done (4ms)
block [235/288] : done (4ms)
block [236/288] : done (4ms)
block [237/288] : done (4ms)
block [238/288] : done (4ms)
block [239/288] : done (4ms)
block [240/288] : done (4ms)
block [241/288] : done (8ms)
block [242/288] : done (15ms)
Chromosome 17 [10 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [243/288] : done (13ms)
block [244/288] : done (4ms)
block [245/288] : done (4ms)
block [246/288] : done (4ms)
block [247/288] : done (4ms)
block [248/288] : done (8ms)
block [249/288] : done (10ms)
block [250/288] : done (4ms)
block [251/288] : done (4ms)
block [252/288] : done (7ms)
Chromosome 18 [9 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [253/288] : done (15ms)
block [254/288] : done (7ms)
block [255/288] : done (4ms)
block [256/288] : done (4ms)
block [257/288] : done (5ms)
block [258/288] : done (4ms)
block [259/288] : done (4ms)
block [260/288] : done (4ms)
block [261/288] : done (4ms)
Chromosome 19 [9 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [262/288] : done (8ms)
block [263/288] : done (4ms)
block [264/288] : done (4ms)
block [265/288] : done (4ms)
block [266/288] : done (4ms)
block [267/288] : done (4ms)
block [268/288] : done (4ms)
block [269/288] : done (4ms)
block [270/288] : done (1ms)
Chromosome 20 [8 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [271/288] : done (8ms)
block [272/288] : done (4ms)
block [273/288] : done (4ms)
block [274/288] : done (4ms)
block [275/288] : done (4ms)
block [276/288] : done (4ms)
block [277/288] : done (4ms)
block [278/288] : done (1ms)
Chromosome 21 [5 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [279/288] : done (9ms)
block [280/288] : done (5ms)
block [281/288] : done (4ms)
block [282/288] : done (4ms)
block [283/288] : done (1ms)
Chromosome 22 [5 blocks in total]
-reading loco predictions for the chromosome...done (0ms)
block [284/288] : done (9ms)
block [285/288] : done (4ms)
block [286/288] : done (4ms)
block [287/288] : done (4ms)
block [288/288] : done (8ms)
Association results stored separately for each trait in files :
* [./output/regenie_step2_asso_WO_PC20_phenotype.regenie]
Number of ignored tests due to low MAC : 18794
Elapsed time : 2.00169s
End time: Tue Jul 22 22:02:49 2025
(regenie_env)
View the result of REGENIE-GWAS¶
head ./output/regenie_step2_asso_WO_PC20_phenotype.regenie | column -t
CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ N TEST BETA SE CHISQ LOG10P EXTRA 1 809876 rs57181708 G A 0.922222 45 ADD 0.819157 0.466077 3.08901 1.10335 NA 1 835499 rs4422948 G A 0.77907 43 ADD 0.344908 0.319173 1.16776 0.553057 NA 1 838555 rs4970383 A C 0.766667 45 ADD 0.00674357 0.29065 0.000538318 0.00811439 NA 1 840753 rs4970382 C T 0.588889 45 ADD 0.0986217 0.23848 0.171018 0.167997 NA 1 846864 rs950122 C G 0.811111 45 ADD 0.234648 0.27831 0.710847 0.39885 NA 1 849998 rs13303222 A G 0.9 45 ADD -0.147105 0.373592 0.155046 0.158791 NA 1 850780 rs6657440 C T 0.7 45 ADD 0.0901261 0.237315 0.144229 0.152358 NA 1 858051 rs4970459 T C 0.8 45 ADD 0.135413 0.294551 0.211347 0.18996 NA 1 866938 rs74047407 A G 0.788889 45 ADD 0.0425628 0.275012 0.0239529 0.056998 NA
# search for the most significant SNP
awk 'NR>1 {print $1,$2,$3,$12}' \
./output/regenie_step2_asso_WO_PC20_phenotype.regenie | sort -k4,4gr 2>/dev/null | head -1 || true
5 78413504 rs3797546 9.13966
# Prepare for plotting the results
regenie_results= data.table::fread("./output/regenie_step2_asso_WO_PC20_phenotype.regenie")
regenie_results[, P := 10^(-LOG10P)] %>%
data.table::setnames(
c("CHROM", "GENPOS", "ID"),
c("CHR", "BP", "SNP")
)
regenie_results %>%
data.table::fwrite("./output/regenie_step2_asso_WO_PC20_phenotype_v2.regenie")
# running about 0.5 minutes
options(repr.plot.width = 16,
repr.plot.height = 4,
repr.plot.res = 600)
source("/home/student/USER/GWAS/data/plotPlink.R")
# plot the results (.regenie is the output file from regenie)
plots= plot_qqman(
plink_assoc_file= "./output/regenie_step2_asso_WO_PC20_phenotype_v2.regenie",
pheno_name= "Standing_height",
save_plot = FALSE,
lambda1_qq_pos = c(1.48, -5.5),
lambda2_qq_pos = c(1.1, -4)
)
print(plots$manhattan_plot)
# running about 0.5 minutes
options(repr.plot.width = 4.1,
repr.plot.height = 4.1,
repr.plot.res = 600)
print(plots$qq_plot)
Part 2: perform regenie analyses with considering the top 20 pcs¶
Step1: fitting the null linear mixed model with regenie¶
For quantitative traits (such as standing height), regenie fits a linear mixed model by default.
It is recommended to inverse normalize the phenotype before analysis to improve normality and statistical power.
# running about 2 minutes
source /home/student/miniconda3/bin/activate regenie_env
regenie \
--step 1 \
--bed /home/student/USER/GWAS/data/European_1w_QC \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--strict \
--bsize 1000 \
--loocv \
--lowmem \
--lowmem-prefix ./output/regenie_tmp_preds \
--apply-rint \
--out ./output/regenie_step1_W_PC20
conda deactivate
(regenie_env) Start time: Sat Jul 19 14:49:02 2025
|===========================|
| REGENIE v4.1.gz |
|===========================|
Copyright (c) 2020-2024 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.
Compiled with Boost Iostream library.
Using Intel MKL with Eigen.
Log of output saved in file : ./output/regenie_step1_W_PC20.log
Options in effect:
--step 1 \
--bed /home/student/USER/GWAS/data/European_1w_QC \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--strict \
--bsize 1000 \
--loocv \
--lowmem \
--lowmem-prefix ./output/regenie_tmp_preds \
--apply-rint \
--out ./output/regenie_step1_W_PC20
Fitting null model
* bim : [/home/student/USER/GWAS/data/European_1w_QC.bim] n_snps = 277265
* fam : [/home/student/USER/GWAS/data/European_1w_QC.fam] n_samples = 10000
* bed : [/home/student/USER/GWAS/data/European_1w_QC.bed]
* phenotypes : [/home/student/USER/GWAS/data/phenotype.txt] n_pheno = 1
-dropping observations with missing values at any of the phenotypes
-number of phenotyped individuals with no missing data = 10000
* covariates : [/home/student/USER/GWAS/data/covar_PCs.txt] n_cov = 20
-number of individuals with covariate data = 10000
* number of individuals used in analysis = 10000
-applying RINT to all phenotypes
* number of observations for each trait:
- 'phenotype': 10000 observations
-residualizing and scaling phenotypes...done (0ms)
* # threads : [31]
* block size : [1000]
* # blocks : [288] for 277265 variants
* # CV folds : [10000]
* ridge data_l0 : [ 5 : 0.01 0.25 0.5 0.75 0.99 ]
* ridge data_l1 : [ 5 : 0.01 0.25 0.5 0.75 0.99 ]
* approximate memory usage : 2GB
* writing level 0 predictions to disk
-temporary files will have prefix [./output/regenie_tmp_preds_l0_Y]
-approximate disk space needed : 110MB
* setting memory...done
Chromosome 1
block [1] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (76ms)
block [2] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (75ms)
block [3] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (118ms)
-calc level 0 ridge...done (82ms)
block [4] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (117ms)
-calc level 0 ridge...done (82ms)
block [5] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (84ms)
block [6] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (85ms)
block [7] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (142ms)
-calc level 0 ridge...done (83ms)
block [8] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (84ms)
block [9] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (82ms)
block [10] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (68ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (82ms)
block [11] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (83ms)
block [12] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (155ms)
-calc level 0 ridge...done (82ms)
block [13] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (169ms)
-calc level 0 ridge...done (81ms)
block [14] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [15] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (81ms)
block [16] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (80ms)
block [17] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [18] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [19] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (119ms)
-calc level 0 ridge...done (82ms)
block [20] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [21] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (82ms)
block [22] : 569 snps (6ms)
-residualizing and scaling genotypes...done (36ms)
-calc working matrices...done (60ms)
-calc level 0 ridge...done (44ms)
Chromosome 2
block [23] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (76ms)
block [24] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (75ms)
block [25] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (118ms)
-calc level 0 ridge...done (77ms)
block [26] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (67ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (75ms)
block [27] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (68ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (75ms)
block [28] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (75ms)
block [29] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (120ms)
-calc level 0 ridge...done (76ms)
block [30] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (75ms)
block [31] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (76ms)
block [32] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (76ms)
block [33] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (76ms)
block [34] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (76ms)
block [35] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (140ms)
-calc level 0 ridge...done (77ms)
block [36] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (68ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (76ms)
block [37] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (67ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (77ms)
block [38] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (68ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (77ms)
block [39] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (69ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (76ms)
block [40] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (76ms)
block [41] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (67ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (76ms)
block [42] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (76ms)
block [43] : 836 snps (13ms)
-residualizing and scaling genotypes...done (50ms)
-calc working matrices...done (116ms)
-calc level 0 ridge...done (66ms)
Chromosome 3
block [44] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (168ms)
-calc level 0 ridge...done (77ms)
block [45] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (119ms)
-calc level 0 ridge...done (76ms)
block [46] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (117ms)
-calc level 0 ridge...done (77ms)
block [47] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (117ms)
-calc level 0 ridge...done (76ms)
block [48] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (73ms)
-calc working matrices...done (137ms)
-calc level 0 ridge...done (83ms)
block [49] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (78ms)
block [50] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (77ms)
block [51] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (70ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (77ms)
block [52] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (77ms)
block [53] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (77ms)
block [54] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (77ms)
block [55] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (77ms)
block [56] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (77ms)
block [57] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (77ms)
block [58] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (77ms)
block [59] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (140ms)
-calc level 0 ridge...done (77ms)
block [60] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (157ms)
-calc level 0 ridge...done (77ms)
block [61] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (198ms)
-calc level 0 ridge...done (78ms)
block [62] : 271 snps (3ms)
-residualizing and scaling genotypes...done (18ms)
-calc working matrices...done (14ms)
-calc level 0 ridge...done (20ms)
Chromosome 4
block [63] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [64] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [65] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [66] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [67] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [68] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [69] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (82ms)
block [70] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [71] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [72] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [73] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (85ms)
block [74] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (138ms)
-calc level 0 ridge...done (83ms)
block [75] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (67ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (81ms)
block [76] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [77] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (67ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [78] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (81ms)
block [79] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [80] : 115 snps (1ms)
-residualizing and scaling genotypes...done (7ms)
-calc working matrices...done (5ms)
-calc level 0 ridge...done (14ms)
Chromosome 5
block [81] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (150ms)
-calc level 0 ridge...done (82ms)
block [82] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (145ms)
-calc level 0 ridge...done (82ms)
block [83] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (177ms)
-calc level 0 ridge...done (81ms)
block [84] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (81ms)
block [85] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [86] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [87] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [88] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [89] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (82ms)
block [90] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (83ms)
block [91] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [92] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (81ms)
block [93] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [94] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (81ms)
block [95] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [96] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [97] : 416 snps (10ms)
-residualizing and scaling genotypes...done (30ms)
-calc working matrices...done (27ms)
-calc level 0 ridge...done (28ms)
Chromosome 6
block [98] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [99] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (82ms)
block [100] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (137ms)
-calc level 0 ridge...done (86ms)
block [101] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (118ms)
-calc level 0 ridge...done (83ms)
block [102] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (117ms)
-calc level 0 ridge...done (83ms)
block [103] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (119ms)
-calc level 0 ridge...done (83ms)
block [104] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (119ms)
-calc level 0 ridge...done (83ms)
block [105] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (83ms)
block [106] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (120ms)
-calc level 0 ridge...done (83ms)
block [107] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (83ms)
block [108] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (83ms)
block [109] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (84ms)
block [110] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (82ms)
block [111] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [112] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [113] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (82ms)
block [114] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (82ms)
block [115] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [116] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [117] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (82ms)
block [118] : 373 snps (4ms)
-residualizing and scaling genotypes...done (23ms)
-calc working matrices...done (30ms)
-calc level 0 ridge...done (26ms)
Chromosome 7
block [119] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [120] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (82ms)
block [121] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [122] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (81ms)
block [123] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (83ms)
block [124] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (83ms)
block [125] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (81ms)
block [126] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (81ms)
block [127] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (82ms)
block [128] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [129] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [130] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (81ms)
block [131] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (80ms)
block [132] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (81ms)
block [133] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (81ms)
block [134] : 265 snps (2ms)
-residualizing and scaling genotypes...done (17ms)
-calc working matrices...done (20ms)
-calc level 0 ridge...done (20ms)
Chromosome 8
block [135] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (82ms)
block [136] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [137] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (155ms)
-calc level 0 ridge...done (82ms)
block [138] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (83ms)
block [139] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [140] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (137ms)
-calc level 0 ridge...done (83ms)
block [141] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [142] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [143] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [144] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (140ms)
-calc level 0 ridge...done (82ms)
block [145] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (83ms)
block [146] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (83ms)
block [147] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [148] : 906 snps (12ms)
-residualizing and scaling genotypes...done (57ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (72ms)
Chromosome 9
block [149] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (83ms)
block [150] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [151] : 1000 snps (24ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (83ms)
block [152] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (142ms)
-calc level 0 ridge...done (82ms)
block [153] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (138ms)
-calc level 0 ridge...done (84ms)
block [154] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (73ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (85ms)
block [155] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [156] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (83ms)
block [157] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (84ms)
block [158] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [159] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [160] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (83ms)
block [161] : 564 snps (9ms)
-residualizing and scaling genotypes...done (35ms)
-calc working matrices...done (48ms)
-calc level 0 ridge...done (41ms)
Chromosome 10
block [162] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (83ms)
block [163] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (84ms)
block [164] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (83ms)
block [165] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (140ms)
-calc level 0 ridge...done (84ms)
block [166] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (83ms)
block [167] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (87ms)
block [168] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (82ms)
block [169] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (147ms)
-calc level 0 ridge...done (83ms)
block [170] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (83ms)
block [171] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [172] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [173] : 1000 snps (19ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [174] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (83ms)
block [175] : 692 snps (11ms)
-residualizing and scaling genotypes...done (42ms)
-calc working matrices...done (75ms)
-calc level 0 ridge...done (55ms)
Chromosome 11
block [176] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [177] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (83ms)
block [178] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (83ms)
block [179] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (83ms)
block [180] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (83ms)
block [181] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (137ms)
-calc level 0 ridge...done (81ms)
block [182] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (83ms)
block [183] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (82ms)
block [184] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (83ms)
block [185] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [186] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [187] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (83ms)
block [188] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (169ms)
-calc level 0 ridge...done (82ms)
block [189] : 711 snps (7ms)
-residualizing and scaling genotypes...done (46ms)
-calc working matrices...done (101ms)
-calc level 0 ridge...done (58ms)
Chromosome 12
block [190] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (81ms)
block [191] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [192] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (81ms)
block [193] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [194] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (81ms)
block [195] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (120ms)
-calc level 0 ridge...done (81ms)
block [196] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (81ms)
block [197] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (81ms)
block [198] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (84ms)
block [199] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (82ms)
block [200] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (81ms)
block [201] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (66ms)
-calc working matrices...done (145ms)
-calc level 0 ridge...done (83ms)
block [202] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (65ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [203] : 453 snps (4ms)
-residualizing and scaling genotypes...done (36ms)
-calc working matrices...done (29ms)
-calc level 0 ridge...done (34ms)
Chromosome 13
block [204] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (122ms)
-calc level 0 ridge...done (82ms)
block [205] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [206] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [207] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (83ms)
block [208] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (123ms)
-calc level 0 ridge...done (83ms)
block [209] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (120ms)
-calc level 0 ridge...done (83ms)
block [210] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (119ms)
-calc level 0 ridge...done (84ms)
block [211] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (83ms)
block [212] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (83ms)
block [213] : 597 snps (6ms)
-residualizing and scaling genotypes...done (39ms)
-calc working matrices...done (51ms)
-calc level 0 ridge...done (47ms)
Chromosome 14
block [214] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (120ms)
-calc level 0 ridge...done (82ms)
block [215] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (121ms)
-calc level 0 ridge...done (82ms)
block [216] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (120ms)
-calc level 0 ridge...done (82ms)
block [217] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (119ms)
-calc level 0 ridge...done (82ms)
block [218] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (62ms)
-calc working matrices...done (120ms)
-calc level 0 ridge...done (82ms)
block [219] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (85ms)
block [220] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (70ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [221] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (69ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (83ms)
block [222] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (70ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (83ms)
block [223] : 1 snps (0ms)
-residualizing and scaling genotypes...done (0ms)
-calc working matrices...done (0ms)
-calc level 0 ridge...done (2ms)
Chromosome 15
block [224] : 1000 snps (30ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (141ms)
-calc level 0 ridge...done (83ms)
block [225] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (82ms)
block [226] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [227] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (82ms)
block [228] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (138ms)
-calc level 0 ridge...done (82ms)
block [229] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (82ms)
block [230] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (83ms)
block [231] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [232] : 680 snps (14ms)
-residualizing and scaling genotypes...done (40ms)
-calc working matrices...done (84ms)
-calc level 0 ridge...done (57ms)
Chromosome 16
block [233] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (124ms)
-calc level 0 ridge...done (84ms)
block [234] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [235] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [236] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [237] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (140ms)
-calc level 0 ridge...done (83ms)
block [238] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [239] : 1000 snps (20ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (83ms)
block [240] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (83ms)
block [241] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (71ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [242] : 907 snps (10ms)
-residualizing and scaling genotypes...done (58ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (87ms)
Chromosome 17
block [243] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (136ms)
-calc level 0 ridge...done (84ms)
block [244] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (146ms)
-calc level 0 ridge...done (86ms)
block [245] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (152ms)
-calc level 0 ridge...done (84ms)
block [246] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (79ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (84ms)
block [247] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (63ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (85ms)
block [248] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (69ms)
-calc working matrices...done (145ms)
-calc level 0 ridge...done (83ms)
block [249] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (68ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [250] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (82ms)
block [251] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (64ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (82ms)
block [252] : 357 snps (4ms)
-residualizing and scaling genotypes...done (21ms)
-calc working matrices...done (71ms)
-calc level 0 ridge...done (24ms)
Chromosome 18
block [253] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (130ms)
-calc level 0 ridge...done (81ms)
block [254] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (80ms)
block [255] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (146ms)
-calc level 0 ridge...done (82ms)
block [256] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (137ms)
-calc level 0 ridge...done (83ms)
block [257] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (138ms)
-calc level 0 ridge...done (83ms)
block [258] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (82ms)
block [259] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (83ms)
block [260] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (83ms)
block [261] : 521 snps (5ms)
-residualizing and scaling genotypes...done (33ms)
-calc working matrices...done (50ms)
-calc level 0 ridge...done (40ms)
Chromosome 19
block [262] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (135ms)
-calc level 0 ridge...done (82ms)
block [263] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (86ms)
block [264] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (72ms)
-calc working matrices...done (134ms)
-calc level 0 ridge...done (83ms)
block [265] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [266] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (139ms)
-calc level 0 ridge...done (83ms)
block [267] : 1000 snps (24ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [268] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (59ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (84ms)
block [269] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (84ms)
block [270] : 363 snps (4ms)
-residualizing and scaling genotypes...done (22ms)
-calc working matrices...done (25ms)
-calc level 0 ridge...done (24ms)
Chromosome 20
block [271] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (83ms)
block [272] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (83ms)
block [273] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (82ms)
block [274] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (127ms)
-calc level 0 ridge...done (82ms)
block [275] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (125ms)
-calc level 0 ridge...done (83ms)
block [276] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (82ms)
block [277] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (131ms)
-calc level 0 ridge...done (82ms)
block [278] : 369 snps (4ms)
-residualizing and scaling genotypes...done (23ms)
-calc working matrices...done (24ms)
-calc level 0 ridge...done (24ms)
Chromosome 21
block [279] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (83ms)
block [280] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (128ms)
-calc level 0 ridge...done (83ms)
block [281] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (129ms)
-calc level 0 ridge...done (83ms)
block [282] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (83ms)
block [283] : 379 snps (4ms)
-residualizing and scaling genotypes...done (24ms)
-calc working matrices...done (28ms)
-calc level 0 ridge...done (25ms)
Chromosome 22
block [284] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (132ms)
-calc level 0 ridge...done (83ms)
block [285] : 1000 snps (21ms)
-residualizing and scaling genotypes...done (61ms)
-calc working matrices...done (148ms)
-calc level 0 ridge...done (82ms)
block [286] : 1000 snps (23ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (126ms)
-calc level 0 ridge...done (83ms)
block [287] : 1000 snps (22ms)
-residualizing and scaling genotypes...done (60ms)
-calc working matrices...done (133ms)
-calc level 0 ridge...done (82ms)
block [288] : 920 snps (20ms)
-residualizing and scaling genotypes...done (54ms)
-calc working matrices...done (137ms)
-calc level 0 ridge...done (81ms)
Level 1 ridge...
-on phenotype 1 (phenotype)...done (351ms)
Output
------
phenotype 1 (phenotype) :
0.01 : Rsq = 0.0304851, MSE = 0.978719
0.25 : Rsq = 0.0402011, MSE = 0.962004<- min value
0.5 : Rsq = 0.0435822, MSE = 0.964436
0.75 : Rsq = 0.0462107, MSE = 0.96748
0.99 : Rsq = 0.0551993, MSE = 0.973247
* making predictions...writing LOCO predictions...done (487ms)
List of blup files written to: [./output/regenie_step1_W_PC20_pred.list]
Elapsed time : 85.6118s
End time: Sat Jul 19 14:50:27 2025
(regenie_env)
See more parameter explanations: https://rgcgithub.github.io/regenie/options/.
Step 2: performing single-variant association tests¶
For quantitative traits (such as standing height), regenie automatically uses a linear mixed model for association testing.
There is no need for saddle point approximation or Firth correction, as these are specific to binary traits.
The output will include effect sizes, standard errors, and p-values for each variant.
# running about 0.5 minutes
source /home/student/miniconda3/bin/activate regenie_env
regenie \
--step 2 \
--bed /home/student/USER/GWAS/data/European_1w_QC \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--out ./output/regenie_step2_asso_W_PC20
conda deactivate
(regenie_env) Start time: Tue Jul 22 14:57:40 2025
|===========================|
| REGENIE v4.1.gz |
|===========================|
Copyright (c) 2020-2024 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.
Compiled with Boost Iostream library.
Using Intel MKL with Eigen.
Log of output saved in file : ./output/regenie_step2_asso_W_PC20.log
Options in effect:
--step 2 \
--bed /home/student/USER/GWAS/data/European_1w_QC \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--out ./output/regenie_step2_asso_W_PC20
Association testing mode with fast multithreading using OpenMP
* bim : [/home/student/USER/GWAS/data/European_1w_QC.bim] n_snps = 277265
* fam : [/home/student/USER/GWAS/data/European_1w_QC.fam] n_samples = 10000
* bed : [/home/student/USER/GWAS/data/European_1w_QC.bed]
* phenotypes : [/home/student/USER/GWAS/data/phenotype.txt] n_pheno = 1
-dropping observations with missing values at any of the phenotypes
-number of phenotyped individuals with no missing data = 10000
* covariates : [/home/student/USER/GWAS/data/covar_PCs.txt] n_cov = 20
-number of individuals with covariate data = 10000
* number of individuals used in analysis = 10000
-applying RINT to all phenotypes
* number of observations for each trait:
- 'phenotype': 10000 observations
* LOCO predictions : [./output/regenie_step1_W_PC20_pred.list]
-file [/home/tch_lz/./output/regenie_step1_W_PC20_1.loco] for phenotype 'phenotype'
-residualizing and scaling phenotypes...done (0ms)
* # threads : [31]
* block size : [1000]
* # blocks : [288]
* approximate memory usage : 231MB
* using minimum MAC of 5 (variants with lower MAC are ignored)
Chromosome 1 [22 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [1/288] : done (18ms)
block [2/288] : done (10ms)
block [3/288] : done (10ms)
block [4/288] : done (10ms)
block [5/288] : done (10ms)
block [6/288] : done (10ms)
block [7/288] : done (10ms)
block [8/288] : done (10ms)
block [9/288] : done (10ms)
block [10/288] : done (10ms)
block [11/288] : done (10ms)
block [12/288] : done (10ms)
block [13/288] : done (10ms)
block [14/288] : done (10ms)
block [15/288] : done (11ms)
block [16/288] : done (10ms)
block [17/288] : done (10ms)
block [18/288] : done (10ms)
block [19/288] : done (10ms)
block [20/288] : done (11ms)
block [21/288] : done (10ms)
block [22/288] : done (8ms)
Chromosome 2 [21 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [23/288] : done (18ms)
block [24/288] : done (12ms)
block [25/288] : done (10ms)
block [26/288] : done (10ms)
block [27/288] : done (10ms)
block [28/288] : done (11ms)
block [29/288] : done (10ms)
block [30/288] : done (10ms)
block [31/288] : done (10ms)
block [32/288] : done (10ms)
block [33/288] : done (10ms)
block [34/288] : done (10ms)
block [35/288] : done (10ms)
block [36/288] : done (10ms)
block [37/288] : done (10ms)
block [38/288] : done (10ms)
block [39/288] : done (10ms)
block [40/288] : done (10ms)
block [41/288] : done (10ms)
block [42/288] : done (10ms)
block [43/288] : done (12ms)
Chromosome 3 [19 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [44/288] : done (14ms)
block [45/288] : done (10ms)
block [46/288] : done (11ms)
block [47/288] : done (10ms)
block [48/288] : done (10ms)
block [49/288] : done (10ms)
block [50/288] : done (10ms)
block [51/288] : done (10ms)
block [52/288] : done (10ms)
block [53/288] : done (10ms)
block [54/288] : done (10ms)
block [55/288] : done (10ms)
block [56/288] : done (10ms)
block [57/288] : done (10ms)
block [58/288] : done (10ms)
block [59/288] : done (10ms)
block [60/288] : done (10ms)
block [61/288] : done (10ms)
block [62/288] : done (4ms)
Chromosome 4 [18 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [63/288] : done (14ms)
block [64/288] : done (10ms)
block [65/288] : done (10ms)
block [66/288] : done (10ms)
block [67/288] : done (10ms)
block [68/288] : done (10ms)
block [69/288] : done (10ms)
block [70/288] : done (10ms)
block [71/288] : done (10ms)
block [72/288] : done (10ms)
block [73/288] : done (12ms)
block [74/288] : done (10ms)
block [75/288] : done (10ms)
block [76/288] : done (10ms)
block [77/288] : done (10ms)
block [78/288] : done (10ms)
block [79/288] : done (10ms)
block [80/288] : done (1ms)
Chromosome 5 [17 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [81/288] : done (14ms)
block [82/288] : done (10ms)
block [83/288] : done (10ms)
block [84/288] : done (10ms)
block [85/288] : done (10ms)
block [86/288] : done (11ms)
block [87/288] : done (16ms)
block [88/288] : done (13ms)
block [89/288] : done (10ms)
block [90/288] : done (10ms)
block [91/288] : done (10ms)
block [92/288] : done (9ms)
block [93/288] : done (10ms)
block [94/288] : done (9ms)
block [95/288] : done (10ms)
block [96/288] : done (9ms)
block [97/288] : done (6ms)
Chromosome 6 [21 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [98/288] : done (14ms)
block [99/288] : done (10ms)
block [100/288] : done (10ms)
block [101/288] : done (10ms)
block [102/288] : done (10ms)
block [103/288] : done (10ms)
block [104/288] : done (10ms)
block [105/288] : done (10ms)
block [106/288] : done (9ms)
block [107/288] : done (10ms)
block [108/288] : done (9ms)
block [109/288] : done (10ms)
block [110/288] : done (9ms)
block [111/288] : done (12ms)
block [112/288] : done (10ms)
block [113/288] : done (9ms)
block [114/288] : done (10ms)
block [115/288] : done (10ms)
block [116/288] : done (10ms)
block [117/288] : done (10ms)
block [118/288] : done (6ms)
Chromosome 7 [16 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [119/288] : done (14ms)
block [120/288] : done (10ms)
block [121/288] : done (10ms)
block [122/288] : done (10ms)
block [123/288] : done (10ms)
block [124/288] : done (14ms)
block [125/288] : done (12ms)
block [126/288] : done (10ms)
block [127/288] : done (9ms)
block [128/288] : done (10ms)
block [129/288] : done (9ms)
block [130/288] : done (10ms)
block [131/288] : done (10ms)
block [132/288] : done (9ms)
block [133/288] : done (10ms)
block [134/288] : done (2ms)
Chromosome 8 [14 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [135/288] : done (13ms)
block [136/288] : done (10ms)
block [137/288] : done (10ms)
block [138/288] : done (10ms)
block [139/288] : done (10ms)
block [140/288] : done (10ms)
block [141/288] : done (10ms)
block [142/288] : done (10ms)
block [143/288] : done (9ms)
block [144/288] : done (10ms)
block [145/288] : done (10ms)
block [146/288] : done (10ms)
block [147/288] : done (10ms)
block [148/288] : done (13ms)
Chromosome 9 [13 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [149/288] : done (15ms)
block [150/288] : done (10ms)
block [151/288] : done (10ms)
block [152/288] : done (10ms)
block [153/288] : done (10ms)
block [154/288] : done (10ms)
block [155/288] : done (10ms)
block [156/288] : done (12ms)
block [157/288] : done (10ms)
block [158/288] : done (10ms)
block [159/288] : done (10ms)
block [160/288] : done (10ms)
block [161/288] : done (8ms)
Chromosome 10 [14 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [162/288] : done (14ms)
block [163/288] : done (10ms)
block [164/288] : done (10ms)
block [165/288] : done (10ms)
block [166/288] : done (10ms)
block [167/288] : done (10ms)
block [168/288] : done (10ms)
block [169/288] : done (10ms)
block [170/288] : done (10ms)
block [171/288] : done (10ms)
block [172/288] : done (10ms)
block [173/288] : done (10ms)
block [174/288] : done (10ms)
block [175/288] : done (10ms)
Chromosome 11 [14 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [176/288] : done (15ms)
block [177/288] : done (10ms)
block [178/288] : done (10ms)
block [179/288] : done (9ms)
block [180/288] : done (10ms)
block [181/288] : done (10ms)
block [182/288] : done (10ms)
block [183/288] : done (10ms)
block [184/288] : done (9ms)
block [185/288] : done (10ms)
block [186/288] : done (9ms)
block [187/288] : done (10ms)
block [188/288] : done (10ms)
block [189/288] : done (10ms)
Chromosome 12 [14 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [190/288] : done (14ms)
block [191/288] : done (10ms)
block [192/288] : done (10ms)
block [193/288] : done (9ms)
block [194/288] : done (10ms)
block [195/288] : done (10ms)
block [196/288] : done (9ms)
block [197/288] : done (10ms)
block [198/288] : done (9ms)
block [199/288] : done (10ms)
block [200/288] : done (12ms)
block [201/288] : done (9ms)
block [202/288] : done (10ms)
block [203/288] : done (6ms)
Chromosome 13 [10 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [204/288] : done (14ms)
block [205/288] : done (10ms)
block [206/288] : done (10ms)
block [207/288] : done (9ms)
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block [209/288] : done (12ms)
block [210/288] : done (10ms)
block [211/288] : done (10ms)
block [212/288] : done (9ms)
block [213/288] : done (9ms)
Chromosome 14 [10 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [214/288] : done (14ms)
block [215/288] : done (10ms)
block [216/288] : done (10ms)
block [217/288] : done (9ms)
block [218/288] : done (10ms)
block [219/288] : done (9ms)
block [220/288] : done (10ms)
block [221/288] : done (10ms)
block [222/288] : done (10ms)
block [223/288] : done (0ms)
Chromosome 15 [9 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [224/288] : done (14ms)
block [225/288] : done (10ms)
block [226/288] : done (10ms)
block [227/288] : done (10ms)
block [228/288] : done (9ms)
block [229/288] : done (10ms)
block [230/288] : done (10ms)
block [231/288] : done (10ms)
block [232/288] : done (9ms)
Chromosome 16 [10 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [233/288] : done (14ms)
block [234/288] : done (10ms)
block [235/288] : done (10ms)
block [236/288] : done (10ms)
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block [239/288] : done (10ms)
block [240/288] : done (9ms)
block [241/288] : done (10ms)
block [242/288] : done (13ms)
Chromosome 17 [10 blocks in total]
-reading loco predictions for the chromosome...done (5ms)
block [243/288] : done (14ms)
block [244/288] : done (10ms)
block [245/288] : done (10ms)
block [246/288] : done (11ms)
block [247/288] : done (9ms)
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block [249/288] : done (9ms)
block [250/288] : done (10ms)
block [251/288] : done (10ms)
block [252/288] : done (3ms)
Chromosome 18 [9 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [253/288] : done (12ms)
block [254/288] : done (10ms)
block [255/288] : done (11ms)
block [256/288] : done (10ms)
block [257/288] : done (11ms)
block [258/288] : done (9ms)
block [259/288] : done (11ms)
block [260/288] : done (10ms)
block [261/288] : done (7ms)
Chromosome 19 [9 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [262/288] : done (13ms)
block [263/288] : done (9ms)
block [264/288] : done (10ms)
block [265/288] : done (9ms)
block [266/288] : done (10ms)
block [267/288] : done (10ms)
block [268/288] : done (10ms)
block [269/288] : done (10ms)
block [270/288] : done (3ms)
Chromosome 20 [8 blocks in total]
-reading loco predictions for the chromosome...done (5ms)
block [271/288] : done (14ms)
block [272/288] : done (10ms)
block [273/288] : done (10ms)
block [274/288] : done (9ms)
block [275/288] : done (10ms)
block [276/288] : done (10ms)
block [277/288] : done (10ms)
block [278/288] : done (3ms)
Chromosome 21 [5 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [279/288] : done (14ms)
block [280/288] : done (9ms)
block [281/288] : done (12ms)
block [282/288] : done (10ms)
block [283/288] : done (4ms)
Chromosome 22 [5 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [284/288] : done (14ms)
block [285/288] : done (9ms)
block [286/288] : done (10ms)
block [287/288] : done (9ms)
block [288/288] : done (13ms)
Association results stored separately for each trait in files :
* [./output/regenie_step2_asso_W_PC20_phenotype.regenie]
Number of ignored tests due to low MAC : 0
Elapsed time : 3.71839s
End time: Tue Jul 22 14:57:44 2025
(regenie_env)
# running about 0.5 minutes
source /home/student/miniconda3/bin/activate regenie_env
regenie \
--step 2 \
--bed /home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--chr 22\
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--out ./output/regenie_step2_asso_W_PC20
conda deactivate
(regenie_env) Start time: Tue Jul 22 14:57:51 2025
|===========================|
| REGENIE v4.1.gz |
|===========================|
Copyright (c) 2020-2024 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.
Compiled with Boost Iostream library.
Using Intel MKL with Eigen.
Log of output saved in file : ./output/regenie_step2_asso_W_PC20.log
Options in effect:
--step 2 \
--bed /home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--chr 22 \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--out ./output/regenie_step2_asso_W_PC20
Association testing mode with fast multithreading using OpenMP
* bim : [/home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp.bim] n_snps = 10396670
* fam : [/home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp.fam] n_samples = 10000
* bed : [/home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp.bed]
* phenotypes : [/home/student/USER/GWAS/data/phenotype.txt] n_pheno = 1
-dropping observations with missing values at any of the phenotypes
-number of phenotyped individuals with no missing data = 10000
* covariates : [/home/student/USER/GWAS/data/covar_PCs.txt] n_cov = 20
-number of individuals with covariate data = 10000
* number of individuals used in analysis = 10000
-applying RINT to all phenotypes
* number of observations for each trait:
- 'phenotype': 10000 observations
* LOCO predictions : [./output/regenie_step1_W_PC20_pred.list]
-file [/home/tch_lz/./output/regenie_step1_W_PC20_1.loco] for phenotype 'phenotype'
-residualizing and scaling phenotypes...done (23ms)
* # threads : [31]
* block size : [1000]
* # blocks : [147]
* approximate memory usage : 201MB
* using minimum MAC of 5 (variants with lower MAC are ignored)
* user specified to test only on select chromosomes
Chromosome 22 [147 blocks in total]
-reading loco predictions for the chromosome...done (4ms)
block [1/147] : done (18ms)
block [2/147] : done (11ms)
block [3/147] : done (10ms)
block [4/147] : done (10ms)
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Association results stored separately for each trait in files :
* [./output/regenie_step2_asso_W_PC20_phenotype.regenie]
Number of ignored tests due to low MAC : 0
Elapsed time : 10.6414s
End time: Tue Jul 22 14:58:01 2025
(regenie_env)
View the result of REGENIE-GWAS¶
head ./output/regenie_step2_asso_W_PC20_phenotype.regenie | column -t
CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ N TEST BETA SE CHISQ LOG10P EXTRA 22 16050822 rs12172168 A G 0.915078 3409 ADD 0.0342386 0.0428313 0.639011 0.372563 NA 22 16051249 rs62224609 C T 0.901309 9930 ADD 0.0178266 0.0233593 0.582395 0.351274 NA 22 16052080 rs4965031 A G 0.941281 2810 ADD 0.0402953 0.056448 0.50958 0.323013 NA 22 16052167 rs375684679 AAAAC A 0.508792 2161 ADD 0.0553284 0.142861 0.149992 0.155807 NA 22 16052962 rs376238049 T C 0.956589 8788 ADD 0.0207208 0.0360476 0.330415 0.247633 NA 22 16053444 rs80167676 T A 0.97472 6685 ADD 0.000972332 0.0533267 0.00033246 0.00636427 NA 22 16053659 rs915675 A C 0.871927 2034 ADD -0.085304 0.0491545 3.0117 1.08268 NA 22 16053730 rs117569664 A C 0.984597 7823 ADD -0.0304404 0.0626845 0.23582 0.202565 NA 22 16053758 rs915677 A G 0.980453 6446 ADD -0.00773713 0.061686 0.0157321 0.0456683 NA
# search for the most significant SNP
awk 'NR>1 {print $1,$2,$3,$12}' \
./output/regenie_step2_asso_W_PC20_phenotype.regenie | sort -k4,4gr 2>/dev/null | head -1 || true
22 17670257 rs78024025 5.00957
# Prepare for plotting the results
library(magrittr)
regenie_results= data.table::fread("./output/regenie_step2_asso_W_PC20_phenotype.regenie")
regenie_results[, P := 10^(-LOG10P)] %>%
data.table::setnames(
c("CHROM", "GENPOS", "ID"),
c("CHR", "BP", "SNP")
)
regenie_results %>%
data.table::fwrite("./output/regenie_step2_asso_W_PC20_phenotype_v2.regenie")
Warning message: “程序包‘magrittr’是用R版本4.4.1 来建造的”
# running about 0.5 minutes
options(repr.plot.width = 16,
repr.plot.height = 4,
repr.plot.res = 600)
source("/home/student/USER/GWAS/data/plotPlink.R")
# plot the results (.regenie is the output file from regenie)
plots= plot_qqman(
plink_assoc_file= "./output/regenie_step2_asso_W_PC20_phenotype_v2.regenie",
pheno_name= "Standing_height",
save_plot = FALSE,
lambda1_qq_pos = c(1.48, -5.5),
lambda2_qq_pos = c(1.1, -4)
)
print(plots$manhattan_plot)
# running about 0.5 minutes
options(repr.plot.width = 4.1,
repr.plot.height = 4.1,
repr.plot.res = 600)
print(plots$qq_plot)
Exercise E : Gene-based testing¶
Instead of performing single-variant association tests, multiple variants can be aggregated in a given region, such as a gene.
This can be especially helpful when testing rare variants as single-vatiant tests usuaally have lower power performance.
To avoid inflation in the gene-based tets due to rare variants as well as reduce computation time, we can implement the collapsing approach of gene-based testing proposed in SAIGE-GENE+, where ultra-rare variants are aggregated into a mask.
Annotation input files: to define variant sets and functional annotations which will be used to generate masks.¶
Each line contains the variant name, the set/gene name and a single annotation category (space/tab separated).
Variants not in this file will be assigned to a default "NULL" category. A maximum of 63 annotation categories (+NULL category) is allowed.
To obtain a single annotation per gene, we could choose the most deleterious functional annotation across the gene transcripts or alternatively use the canonical transcript (note that its definition can vary across software).
head /home/student/USER/GWAS/data/anno_file.txt | column -t
rs2334338 U6 Noncoding 22:16144238_CT_C U6 Noncoding rs529750096 ABCD1P4 Noncoding rs7285246 PABPC1P9 Noncoding rs9617234 SLC9B1P4 Noncoding rs201639724 SLC9B1P4 Noncoding rs565789739 SLC9B1P4 Noncoding 22:16432988_GTACT_G SLC9B1P4 Noncoding 22:16434935_TCCTAA_T SLC9B1P4 Noncoding rs9617238 SLC9B1P4 Noncoding
Set list file: to list variants within each set/gene to use when building masks.¶
Each line contains the set/gene name followed by a chromosome and physical position for the set/gene, then by a comma-separated list of variants included in the set/gene.
head /home/student/USER/GWAS/data/set_list.txt | column -t
U6 22 16143946 rs2334338,22:16144238_CT_C ABCD1P4 22 16384531 rs529750096 PABPC1P9 22 16425814 rs7285246 SLC9B1P4 22 16429472 rs9617234,rs201639724,rs565789739,22:16432988_GTACT_G,22:16434935_TCCTAA_T,rs9617238,rs2212194,rs202204800,rs9617244,rs200596554,rs201265605,rs199810539,rs572119925,rs2000508,rs78350717,rs201369337,rs200639740,rs367744914,rs200741211,rs201464764,rs11167316,rs370772954,rs2236636,rs2078653,rs8184977,rs8135765,rs200598360,rs7288502,rs7287695,rs201141516,rs200197183,rs12628801 ACTR3BP6 22 16482298 rs7510928,rs2027643,rs373129713,rs2268774,22:16490252_CT_C,rs9617160,rs1807637 CHEK2P4 22 16498387 rs2186521,rs200058026,rs7287988,rs6010332,rs11167331,rs2212222,rs6010340,rs201979747,rs4911646,rs12053778,rs2309185,rs200691663 KCNMB3P1 22 16578328 rs564070021,rs370487180 CCT8L2 22 16586715 rs2154927,rs201451756,rs6010291,rs4350859,rs117347043,rs117578132 TPTEP1 22 16601412 rs138900103,rs5771521,rs1988773,rs5771523,rs9617185,rs4911743,rs372890903,rs142722313,rs369554167,rs200911774,rs202061916,rs373703032,rs4530463,rs9617332,rs2212249,rs200140724,rs142850344,rs4437073,rs538385206,rs4426619,rs2212259,rs9617335,rs9617195,rs2078654,rs201053955,rs192479180,rs376053300,rs80319087,rs4911763,rs4911767,rs5771551,rs202107298,rs2186539,rs12628324,rs62221827,rs8139924,rs131509,rs131510,rs131514,rs374792244,rs12628716,rs5771591,rs3016106 SLC25A15P5 22 16645749 rs5771409
Mask file¶
This file specifies which annotation categories should be combined into masks.
Each line contains a mask name followed by a comma-separated list of categories included in the mask (i.e. union is taken over categories).
head /home/student/USER/GWAS/data/mask_file.txt | column -t
LoF LoF LoF_Splice_Region LoF,Splice_Region Damaging_All LoF,Splice_Region,Missense Missense_All Missense Splice_Region Splice_Region Synonymous Synonymous Noncoding Noncoding
Checking input files¶
To assess the concordance between the input files for building masks, we can use --check-burden-files which will generate a report in file_masks_report.txt containing:
for each set, the list the variants in the set-list file which are unrecognized (not genotyped or not present in annotation file for the set)
for each mask, the list of annotations in the mask definition file which are not in the annotation file
Additionally, we can use --strict-check-burden to enforce full agreement between the three files (if not, program will terminate) :
all genotyped variants in the set list file must be in the annotation file (for the corresponding set)
all annotations in the mask definition file must be present in the annotation file
source /home/student/miniconda3/bin/activate regenie_env
regenie \
--step 2 \
--bed /home/student/USER/GWAS/data/European_1w \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--check-burden-files \
--anno-file /home/student/USER/GWAS/data/anno_file.txt \
--set-list /home/student/USER/GWAS/data/set_list.txt \
--mask-def /home/student/USER/GWAS/data/mask_file.txt \
--skip-test \
--strict-check-burden \
--out ./output/burden_check
conda deactivate
(regenie_env) Start time: Tue Jul 22 14:59:04 2025
|===========================|
| REGENIE v4.1.gz |
|===========================|
Copyright (c) 2020-2024 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.
Compiled with Boost Iostream library.
Using Intel MKL with Eigen.
Log of output saved in file : ./output/burden_check.log
Options in effect:
--step 2 \
--bed /home/student/USER/GWAS/data/European_1w \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--check-burden-files \
--anno-file /home/student/USER/GWAS/data/anno_file.txt \
--set-list /home/student/USER/GWAS/data/set_list.txt \
--mask-def /home/student/USER/GWAS/data/mask_file.txt \
--strict-check-burden \
--out ./output/burden_check
Association testing mode (joint tests) with fast multithreading using OpenMP
* bim : [/home/student/USER/GWAS/data/European_1w.bim] n_snps = 784256
* fam : [/home/student/USER/GWAS/data/European_1w.fam] n_samples = 10000
* bed : [/home/student/USER/GWAS/data/European_1w.bed]
* phenotypes : [/home/student/USER/GWAS/data/phenotype.txt] n_pheno = 1
-dropping observations with missing values at any of the phenotypes
-number of phenotyped individuals with no missing data = 10000
* covariates : [/home/student/USER/GWAS/data/covar_PCs.txt] n_cov = 20
-number of individuals with covariate data = 10000
* number of individuals used in analysis = 10000
-applying RINT to all phenotypes
* number of observations for each trait:
- 'phenotype': 10000 observations
* LOCO predictions : [./output/regenie_step1_W_PC20_pred.list]
-file [/home/tch_lz/./output/regenie_step1_W_PC20_1.loco] for phenotype 'phenotype'
-residualizing and scaling phenotypes...done (0ms)
* annotations : [/home/student/USER/GWAS/data/anno_file.txt]
+number of annotations categories = 6
* masks : [/home/student/USER/GWAS/data/mask_file.txt] n_masks = 7
* aaf cutoffs : [ 1 : 0.01 ] + singletons
* set file : [/home/student/USER/GWAS/data/set_list.txt] n_sets = 478
WARNING: Detected 476 sets with variants not in genetic data or annotation files.
WARNING: Detected 205 sets with only unknown variants (these are ignored).
+report on burden input files written to [./output/burden_check_masks_report.txt]
* # threads : [31]
* # tested sets : [478]
* max block size : [1000]
* rule used to build masks : max
* approximate memory usage : 349MB
* using minimum MAC of 5 (masks with lower MAC are ignored)
Chromosome 22 [478 sets in total]
-reading loco predictions for the chromosome...done (4ms)
set [1/478] : CCT8L2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [2/478] : IL17RA - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [3/478] : LINC01664 - 2 variants...
-reading in genotypes and building masks...done (1ms)
set [4/478] : HDHD5 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [5/478] : ADA2 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [6/478] : CECR3 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [7/478] : CECR2 - 30 variants...
-reading in genotypes and building masks...done (0ms)
set [8/478] : SLC25A18 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [9/478] : ATP6V1E1 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [10/478] : BCL2L13 - 24 variants...
-reading in genotypes and building masks...done (0ms)
set [11/478] : BID - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [12/478] : MICAL3 - 36 variants...
-reading in genotypes and building masks...done (0ms)
set [13/478] : LINC01634 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [14/478] : PEX26 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [15/478] : TUBA8 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [16/478] : USP18 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [17/478] : FAM230D - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [18/478] : FAM230A - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [19/478] : GGTLC5P - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [20/478] : FAM230J - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [21/478] : FAM247B - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [22/478] : GGTLC3 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [23/478] : TMEM191B - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [24/478] : PI4KAP1 - 18 variants...
-reading in genotypes and building masks...done (0ms)
set [25/478] : RIMBP3 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [26/478] : Metazoa_SRP - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [27/478] : FAM246B - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [28/478] : CA15P2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [29/478] : PPP1R26P2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [30/478] : FAM230F - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [31/478] : DGCR6 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [32/478] : PRODH - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [33/478] : DGCR2 - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [34/478] : ESS2 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [35/478] : GSC2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [36/478] : CLTCL1 - 9 variants...
-reading in genotypes and building masks...done (0ms)
set [37/478] : HIRA - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [38/478] : MRPL40 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [39/478] : UFD1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [40/478] : CDC45 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [41/478] : LINC00895 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [42/478] : SEPTIN5 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [43/478] : GP1BB - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [44/478] : TBX1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [45/478] : GNB1L - 12 variants...
-reading in genotypes and building masks...done (0ms)
set [46/478] : RTL10 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [47/478] : TXNRD2 - 13 variants...
-reading in genotypes and building masks...done (0ms)
set [48/478] : COMT - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [49/478] : ARVCF - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [50/478] : TANGO2 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [51/478] : DGCR8 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [52/478] : TRMT2A - 1 variants...
-reading in genotypes and building masks...done (1ms)
set [53/478] : LINC02891 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [54/478] : LINC00896 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [55/478] : RTN4R - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [56/478] : KLHL22 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [57/478] : PI4KA - 17 variants...
-reading in genotypes and building masks...done (0ms)
set [58/478] : SNAP29 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [59/478] : CRKL - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [60/478] : LINC01637 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [61/478] : AIFM3 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [62/478] : LZTR1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [63/478] : THAP7 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [64/478] : P2RX6 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [65/478] : LRRC74B - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [66/478] : E2F6P2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [67/478] : FAM230B - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [68/478] : FAM230H - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [69/478] : PPP1R26P5 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [70/478] : FAM246A - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [71/478] : RIMBP3B - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [72/478] : HIC2 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [73/478] : MAPK1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [74/478] : PPM1F - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [75/478] : PRAMENP - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [76/478] : IGLVIV-66-1 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [77/478] : IGLVV-66 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [78/478] : IGLVI-63 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [79/478] : ABHD17AP5 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [80/478] : IGLV4-60 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [81/478] : IGLV10-54 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [82/478] : BMS1P20 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [83/478] : IGLV5-52 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [84/478] : ASH2LP3 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [85/478] : IGLV9-49 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [86/478] : IGLV5-48 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [87/478] : IGLV1-47 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [88/478] : IGLV1-44 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [89/478] : IGLV7-43 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [90/478] : IGLV1-41 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [91/478] : ASH2LP1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [92/478] : IGLV5-37 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [93/478] : IGLV1-36 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [94/478] : ASH2LP4 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [95/478] : IGLV7-35 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [96/478] : ZNF280B - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [97/478] : ZNF280A - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [98/478] : PRAME - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [99/478] : LL22NC03-63E9.3 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [100/478] : IGLV2-34 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [101/478] : IGLV3-32 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [102/478] : IGLV3-30 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [103/478] : IGLV3-25 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [104/478] : IGLV2-23 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [105/478] : IGLV3-22 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [106/478] : IGLV3-21 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [107/478] : IGLV2-18 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [108/478] : IGLV3-16 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [109/478] : IGLV3-15 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [110/478] : IGLV2-14 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [111/478] : IGLV3-12 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [112/478] : IGLV3-10 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [113/478] : IGLV3-7 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [114/478] : IGLV4-3 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [115/478] : IGLV3-1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [116/478] : IGLL5 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [117/478] : IGLC3 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [118/478] : IGLJ5 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [119/478] : IGLC7 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [120/478] : RSPH14 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [121/478] : GNAZ - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [122/478] : BCR - 13 variants...
-reading in genotypes and building masks...done (0ms)
set [123/478] : ZDHHC8BP - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [124/478] : LINC01659 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [125/478] : FAM230I - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [126/478] : PCAT14 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [127/478] : DRICH1 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [128/478] : GUSBP11 - 11 variants...
-reading in genotypes and building masks...done (0ms)
set [129/478] : RGL4 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [130/478] : ZNF70 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [131/478] : VPREB3 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [132/478] : CHCHD10 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [133/478] : MMP11 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [134/478] : SMARCB1 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [135/478] : DERL3 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [136/478] : SLC2A11 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [137/478] : MIF - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [138/478] : GSTT2B - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [139/478] : GSTT2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [140/478] : CABIN1 - 13 variants...
-reading in genotypes and building masks...done (0ms)
set [141/478] : SUSD2 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [142/478] : GGT5 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [143/478] : POM121L9P - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [144/478] : SPECC1L - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [145/478] : ADORA2A - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [146/478] : ADORA2A-AS1 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [147/478] : GUCD1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [148/478] : SNRPD3 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [149/478] : GGT1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [150/478] : PIWIL3 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [151/478] : SGSM1 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [152/478] : LHFPL7 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [153/478] : KIAA1671 - 20 variants...
-reading in genotypes and building masks...done (0ms)
set [154/478] : CRYBB3 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [155/478] : CRYBB2 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [156/478] : CRYBB2P1 - 10 variants...
-reading in genotypes and building masks...done (0ms)
set [157/478] : GRK3-AS1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [158/478] : GRK3 - 28 variants...
-reading in genotypes and building masks...done (0ms)
set [159/478] : MYO18B - 30 variants...
-reading in genotypes and building masks...done (0ms)
set [160/478] : LINC02559 - 15 variants...
-reading in genotypes and building masks...done (0ms)
set [161/478] : SEZ6L - 40 variants...
-reading in genotypes and building masks...done (0ms)
set [162/478] : RPS3AP55 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [163/478] : ASPHD2 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [164/478] : TFIP11 - 1 variants...
-reading in genotypes and building masks...done (2ms)
set [165/478] : TPST2 - 11 variants...
-reading in genotypes and building masks...done (0ms)
set [166/478] : CRYBA4 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [167/478] : MIAT - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [168/478] : MIATNB - 49 variants...
-reading in genotypes and building masks...done (0ms)
set [169/478] : LINC01638 - 12 variants...
-reading in genotypes and building masks...done (0ms)
set [170/478] : LINC02554 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [171/478] : CPMER - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [172/478] : MN1 - 11 variants...
-reading in genotypes and building masks...done (0ms)
set [173/478] : PITPNB - 12 variants...
-reading in genotypes and building masks...done (0ms)
set [174/478] : TTC28-AS1 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [175/478] : TTC28 - 60 variants...
-reading in genotypes and building masks...done (1ms)
set [176/478] : CHEK2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [177/478] : HSCB - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [178/478] : CCDC117 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [179/478] : XBP1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [180/478] : ZNRF3 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [181/478] : KREMEN1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [182/478] : RNU6-1219P - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [183/478] : EMID1 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [184/478] : RHBDD3 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [185/478] : EWSR1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [186/478] : RASL10A - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [187/478] : AP1B1 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [188/478] : RFPL1S - 9 variants...
-reading in genotypes and building masks...done (0ms)
set [189/478] : NEFH - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [190/478] : THOC5 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [191/478] : NIPSNAP1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [192/478] : NF2 - 9 variants...
-reading in genotypes and building masks...done (0ms)
set [193/478] : CABP7 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [194/478] : ZMAT5 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [195/478] : UQCR10 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [196/478] : ASCC2 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [197/478] : MTMR3 - 11 variants...
-reading in genotypes and building masks...done (0ms)
set [198/478] : HORMAD2-AS1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [199/478] : HORMAD2 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [200/478] : TBC1D10A - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [201/478] : SF3A1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [202/478] : RNF215 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [203/478] : SEC14L2 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [204/478] : GAL3ST1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [205/478] : PES1 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [206/478] : TCN2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [207/478] : RPL13AP26 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [208/478] : DUSP18 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [209/478] : OSBP2 - 23 variants...
-reading in genotypes and building masks...done (0ms)
set [210/478] : MORC2-AS1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [211/478] : MORC2 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [212/478] : TUG1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [213/478] : SMTN - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [214/478] : RPS15AP37 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [215/478] : PLA2G3 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [216/478] : SNRPNP2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [217/478] : RNF185 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [218/478] : LIMK2 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [219/478] : PIK3IP1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [220/478] : PIK3IP1-DT - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [221/478] : DRG1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [222/478] : EIF4ENIF1 - 9 variants...
-reading in genotypes and building masks...done (0ms)
set [223/478] : SFI1 - 17 variants...
-reading in genotypes and building masks...done (0ms)
set [224/478] : PISD - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [225/478] : PRR14L - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [226/478] : DEPDC5 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [227/478] : YWHAH-AS1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [228/478] : LINC02558 - 11 variants...
-reading in genotypes and building masks...done (0ms)
set [229/478] : RN7SL305P - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [230/478] : SLC5A1 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [231/478] : AP1B1P1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [232/478] : C22orf42 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [233/478] : RFPL2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [234/478] : SLC5A4-AS1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [235/478] : SLC5A4 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [236/478] : RFPL3S - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [237/478] : BPIFC - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [238/478] : FBXO7 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [239/478] : SYN3 - 73 variants...
-reading in genotypes and building masks...done (0ms)
set [240/478] : TIMP3 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [241/478] : LINC01640 - 9 variants...
-reading in genotypes and building masks...done (0ms)
set [242/478] : LARGE1 - 69 variants...
-reading in genotypes and building masks...done (0ms)
set [243/478] : LINC01643 - 24 variants...
-reading in genotypes and building masks...done (0ms)
set [244/478] : ACO2P1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [245/478] : LINC02885 - 26 variants...
-reading in genotypes and building masks...done (0ms)
set [246/478] : ISX - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [247/478] : LINC01399 - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [248/478] : HMGXB4 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [249/478] : TOM1 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [250/478] : HMOX1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [251/478] : MCM5 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [252/478] : RASD2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [253/478] : MB - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [254/478] : APOL6 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [255/478] : MRPS16P3 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [256/478] : APOL5 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [257/478] : RBFOX2 - 43 variants...
-reading in genotypes and building masks...done (0ms)
set [258/478] : APOL3 - 1 variants...
-reading in genotypes and building masks...done (2ms)
set [259/478] : MTND1P10 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [260/478] : APOL4 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [261/478] : APOL2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [262/478] : APOL1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [263/478] : MYH9 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [264/478] : MYH9-DT - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [265/478] : Y_RNA - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [266/478] : TXN2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [267/478] : EIF3D - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [268/478] : CACNG2 - 47 variants...
-reading in genotypes and building masks...done (0ms)
set [269/478] : CACNG2-DT - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [270/478] : IFT27 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [271/478] : PVALB - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [272/478] : NCF4-AS1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [273/478] : NCF4 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [274/478] : CSF2RB - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [275/478] : LL22NC01-81G9.3 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [276/478] : CIMIP4 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [277/478] : TST - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [278/478] : MPST - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [279/478] : KCTD17 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [280/478] : TMPRSS6 - 10 variants...
-reading in genotypes and building masks...done (0ms)
set [281/478] : IL2RB - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [282/478] : C1QTNF6 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [283/478] : SSTR3 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [284/478] : RAC2 - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [285/478] : CYTH4 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [286/478] : ELFN2 - 19 variants...
-reading in genotypes and building masks...done (0ms)
set [287/478] : MFNG - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [288/478] : CARD10 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [289/478] : CDC42EP1 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [290/478] : LGALS2 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [291/478] : GGA1 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [292/478] : PDXP - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [293/478] : LGALS1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [294/478] : NOL12 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [295/478] : TRIOBP - 15 variants...
-reading in genotypes and building masks...done (0ms)
set [296/478] : GCAT - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [297/478] : ANKRD54 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [298/478] : EIF3L - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [299/478] : MICALL1 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [300/478] : C22orf23 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [301/478] : POLR2F - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [302/478] : SOX10 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [303/478] : PICK1 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [304/478] : BAIAP2L2 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [305/478] : PLA2G6 - 9 variants...
-reading in genotypes and building masks...done (0ms)
set [306/478] : MAFF - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [307/478] : TMEM184B - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [308/478] : CSNK1E - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [309/478] : KCNJ4 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [310/478] : KDELR3 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [311/478] : DMC1 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [312/478] : FAM227A - 11 variants...
-reading in genotypes and building masks...done (0ms)
set [313/478] : CBY1 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [314/478] : TOMM22 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [315/478] : JOSD1 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [316/478] : GTPBP1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [317/478] : SUN2 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [318/478] : DNAL4 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [319/478] : NPTXR - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [320/478] : CBX6 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [321/478] : APOBEC3A - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [322/478] : APOBEC3B - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [323/478] : APOBEC3C - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [324/478] : APOBEC3D - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [325/478] : APOBEC3F - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [326/478] : APOBEC3H - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [327/478] : COX5BP7 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [328/478] : PDGFB - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [329/478] : RPL3 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [330/478] : SYNGR1 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [331/478] : TAB1 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [332/478] : MGAT3 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [333/478] : MIEF1 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [334/478] : ATF4 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [335/478] : RPS19BP1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [336/478] : CACNA1I - 17 variants...
-reading in genotypes and building masks...done (0ms)
set [337/478] : ENTHD1 - 14 variants...
-reading in genotypes and building masks...done (0ms)
set [338/478] : GRAP2 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [339/478] : FAM83F - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [340/478] : TNRC6B - 11 variants...
-reading in genotypes and building masks...done (0ms)
set [341/478] : RPL7P52 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [342/478] : ADSL - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [343/478] : SGSM3 - 3 variants...
-reading in genotypes and building masks...done (1ms)
set [344/478] : MRTFA - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [345/478] : SLC25A17 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [346/478] : ST13 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [347/478] : XPNPEP3 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [348/478] : RBX1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [349/478] : RPS9P2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [350/478] : ACTBP15 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [351/478] : EP300 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [352/478] : L3MBTL2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [353/478] : RANGAP1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [354/478] : ZC3H7B - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [355/478] : TEF - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [356/478] : TOB2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [357/478] : ACO2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [358/478] : PHF5A - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [359/478] : POLR3H - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [360/478] : CSDC2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [361/478] : PMM1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [362/478] : DESI1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [363/478] : XRCC6 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [364/478] : MEI1 - 10 variants...
-reading in genotypes and building masks...done (0ms)
set [365/478] : SREBF2 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [366/478] : TNFRSF13C - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [367/478] : CENPM - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [368/478] : WBP2NL - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [369/478] : NAGA - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [370/478] : NDUFA6 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [371/478] : NDUFA6-DT - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [372/478] : CYP2D6 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [373/478] : CYP2D7 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [374/478] : CYP2D8P - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [375/478] : TCF20 - 17 variants...
-reading in genotypes and building masks...done (0ms)
set [376/478] : OGFRP1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [377/478] : LINC01315 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [378/478] : NFAM1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [379/478] : RRP7A - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [380/478] : SERHL2 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [381/478] : POLDIP3 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [382/478] : CYB5R3 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [383/478] : A4GALT - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [384/478] : RPL5P34 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [385/478] : GOLGA2P4 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [386/478] : ARFGAP3 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [387/478] : PACSIN2 - 21 variants...
-reading in genotypes and building masks...done (0ms)
set [388/478] : TTLL1-AS1 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [389/478] : TTLL1 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [390/478] : BIK - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [391/478] : MCAT - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [392/478] : TSPO - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [393/478] : TTLL12 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [394/478] : SCUBE1 - 10 variants...
-reading in genotypes and building masks...done (0ms)
set [395/478] : LINC01639 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [396/478] : MPPED1 - 13 variants...
-reading in genotypes and building masks...done (0ms)
set [397/478] : EFCAB6-AS1 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [398/478] : EFCAB6 - 45 variants...
-reading in genotypes and building masks...done (0ms)
set [399/478] : SULT4A1 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [400/478] : PNPLA5 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [401/478] : PNPLA3 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [402/478] : SAMM50 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [403/478] : PARVB - 12 variants...
-reading in genotypes and building masks...done (0ms)
set [404/478] : PARVG - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [405/478] : SHISAL1 - 14 variants...
-reading in genotypes and building masks...done (0ms)
set [406/478] : SKP1P4 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [407/478] : LINC01656 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [408/478] : RTL6 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [409/478] : KRT18P23 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [410/478] : LINC00207 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [411/478] : LINC00229 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [412/478] : ANP32BP2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [413/478] : PRR5 - 17 variants...
-reading in genotypes and building masks...done (0ms)
set [414/478] : ARHGAP8 - 28 variants...
-reading in genotypes and building masks...done (0ms)
set [415/478] : PHF21B - 17 variants...
-reading in genotypes and building masks...done (0ms)
set [416/478] : NUP50-DT - 9 variants...
-reading in genotypes and building masks...done (0ms)
set [417/478] : NUP50 - 9 variants...
-reading in genotypes and building masks...done (0ms)
set [418/478] : KIAA0930 - 16 variants...
-reading in genotypes and building masks...done (0ms)
set [419/478] : UPK3A - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [420/478] : FAM118A - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [421/478] : SMC1B - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [422/478] : RIBC2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [423/478] : FBLN1 - 13 variants...
-reading in genotypes and building masks...done (0ms)
set [424/478] : LINC01589 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [425/478] : ATXN10 - 20 variants...
-reading in genotypes and building masks...done (0ms)
set [426/478] : WNT7B - 13 variants...
-reading in genotypes and building masks...done (0ms)
set [427/478] : LINC00899 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [428/478] : MIRLET7BHG - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [429/478] : PPARA - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [430/478] : CDPF1 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [431/478] : PKDREJ - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [432/478] : TTC38 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [433/478] : GTSE1 - 12 variants...
-reading in genotypes and building masks...done (0ms)
set [434/478] : TRMU - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [435/478] : CELSR1 - 31 variants...
-reading in genotypes and building masks...done (0ms)
set [436/478] : GRAMD4 - 14 variants...
-reading in genotypes and building masks...done (0ms)
set [437/478] : CERK - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [438/478] : TBC1D22A - 69 variants...
-reading in genotypes and building masks...done (0ms)
set [439/478] : LINC01644 - 16 variants...
-reading in genotypes and building masks...done (0ms)
set [440/478] : EPIC1 - 47 variants...
-reading in genotypes and building masks...done (0ms)
set [441/478] : MIR3201 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [442/478] : TAFA5 - 83 variants...
-reading in genotypes and building masks...done (0ms)
set [443/478] : LINC01310 - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [444/478] : NHIP - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [445/478] : MIR3667HG - 54 variants...
-reading in genotypes and building masks...done (2ms)
set [446/478] : RPL5P35 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [447/478] : BRD1 - 16 variants...
-reading in genotypes and building masks...done (0ms)
set [448/478] : ZBED4 - 10 variants...
-reading in genotypes and building masks...done (0ms)
set [449/478] : ALG12 - 5 variants...
-reading in genotypes and building masks...done (0ms)
set [450/478] : CRELD2 - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [451/478] : PIM3 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [452/478] : IL17REL - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [453/478] : TTLL8 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [454/478] : MLC1 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [455/478] : MOV10L1 - 15 variants...
-reading in genotypes and building masks...done (0ms)
set [456/478] : PANX2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [457/478] : TRABD - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [458/478] : SELENOO - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [459/478] : TUBGCP6 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [460/478] : MAPK12 - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [461/478] : PLXNB2 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [462/478] : DENND6B - 8 variants...
-reading in genotypes and building masks...done (0ms)
set [463/478] : PPP6R2 - 10 variants...
-reading in genotypes and building masks...done (0ms)
set [464/478] : SBF1 - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [465/478] : ADM2 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [466/478] : MIOX - 7 variants...
-reading in genotypes and building masks...done (0ms)
set [467/478] : LMF2 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [468/478] : NCAPH2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [469/478] : SCO2 - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [470/478] : SYCE3 - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [471/478] : CPT1B - 6 variants...
-reading in genotypes and building masks...done (0ms)
set [472/478] : CHKB - 3 variants...
-reading in genotypes and building masks...done (0ms)
set [473/478] : CHKB-DT - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [474/478] : MAPK8IP2 - 4 variants...
-reading in genotypes and building masks...done (0ms)
set [475/478] : ARSA - 1 variants...
-reading in genotypes and building masks...done (0ms)
set [476/478] : SHANK3 - 12 variants...
-reading in genotypes and building masks...done (0ms)
set [477/478] : ACR - 2 variants...
-reading in genotypes and building masks...done (0ms)
set [478/478] : RABL2B - 1 variants...
-reading in genotypes and building masks...done (0ms)
Association results stored separately for each trait in files :
* [./output/burden_check_phenotype.regenie]
Number of ignored tests due to low MAC : 0
Elapsed time : 1.94643s
End time: Tue Jul 22 14:59:06 2025
(regenie_env)
source /home/student/miniconda3/bin/activate regenie_env
regenie \
--step 2 \
--bed /home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--chr 22\
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--check-burden-files \
--anno-file /home/student/USER/GWAS/data/anno_file.txt \
--set-list /home/student/USER/GWAS/data/set_list.txt \
--mask-def /home/student/USER/GWAS/data/mask_file.txt \
--skip-test \
--strict-check-burden \
--out ./output/burden_check
conda deactivate
(regenie_env) Start time: Tue Jul 22 15:09:08 2025
|===========================|
| REGENIE v4.1.gz |
|===========================|
Copyright (c) 2020-2024 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.
Compiled with Boost Iostream library.
Using Intel MKL with Eigen.
Log of output saved in file : ./output/burden_check.log
Options in effect:
--step 2 \
--bed /home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--chr 22 \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--check-burden-files \
--anno-file /home/student/USER/GWAS/data/anno_file.txt \
--set-list /home/student/USER/GWAS/data/set_list.txt \
--mask-def /home/student/USER/GWAS/data/mask_file.txt \
--strict-check-burden \
--out ./output/burden_check
Association testing mode (joint tests) with fast multithreading using OpenMP
* bim : [/home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp.bim] n_snps = 10396670
* fam : [/home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp.fam] n_samples = 10000
* bed : [/home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp.bed]
* phenotypes : [/home/student/USER/GWAS/data/phenotype.txt] n_pheno = 1
-dropping observations with missing values at any of the phenotypes
-number of phenotyped individuals with no missing data = 10000
* covariates : [/home/student/USER/GWAS/data/covar_PCs.txt] n_cov = 20
-number of individuals with covariate data = 10000
* number of individuals used in analysis = 10000
-applying RINT to all phenotypes
* number of observations for each trait:
- 'phenotype': 10000 observations
* LOCO predictions : [./output/regenie_step1_W_PC20_pred.list]
-file [/home/tch_lz/./output/regenie_step1_W_PC20_1.loco] for phenotype 'phenotype'
-residualizing and scaling phenotypes...done (0ms)
* annotations : [/home/student/USER/GWAS/data/anno_file.txt]
+number of annotations categories = 6
* masks : [/home/student/USER/GWAS/data/mask_file.txt] n_masks = 7
* aaf cutoffs : [ 1 : 0.01 ] + singletons
* set file : [/home/student/USER/GWAS/data/set_list.txt] n_sets = 683
WARNING: Detected 1 sets with variants not in genetic data or annotation files.
+report on burden input files written to [./output/burden_check_masks_report.txt]
ERROR: Annotation/Set list/Mask definition files don't agree. Check report for details.
(regenie_env)
AAF file¶
Both functional annotations and alternative allele frequency (AAF) cutoffs are used when building masks (e.g. only considering LoF sites where AAF is below 1%).
By default, the AAF for each variant is computed from the sample but alternatively, the user can specify variant AAFs using this file.
AAF cutoffs¶
Option --aaf-bins specifies the AAF upper bounds used to generate burden masks (AAF and not MAF [minor allele frequency] is used when deciding which variants go into a mask).
By default, a mask based on singleton sites are always included.
For example, --aaf-bins 0.01,0.05 will generate 3 burden masks for AAFs in [0,0.01], [0,0.05] and singletons.
SKAT/ACAT tests¶
The option --vc-tests is used to specify the gene-based tests to run. By default, these tests use all variants in each mask category.
If you'd like to only include variants whose AAF is below a given threshold ,e.g. only including rare variants, you can use --vc-maxAAF.
For example, --vc-tests skato,acato-full will run SKATO and ACATO (both using the default grid of 8 rho values for the SKATO models) and the p-values for SKAT, SKATO, ACATV and ACATO will be output.
Ultra-rare variants (defined by default as MAC ≤ 10, see --vc-MACthr) are collapsed into a burden mask which is then included in the tests instead of the individual variants.
Joint test for burden masks¶
The ACAT test combines the p-values of the individual burden masks using the Cauchy combination method.
If you only want to output the results for the joint tests (ignore the marginal tests), use --joint-only.
source /home/student/miniconda3/bin/activate regenie_env
regenie \
--step 2 \
--bed /home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp \
--chr 22 \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--anno-file /home/student/USER/GWAS/data/anno_file.txt \
--set-list /home/student/USER/GWAS/data/set_list.txt \
--mask-def /home/student/USER/GWAS/data/mask_file.txt \
--rgc-gene-p \
--vc-tests skato,acato-full \
--joint acat,sbat \
--vc-MACthr 10 \
--out ./output/gene_based_testing
conda deactivate
(regenie_env) Start time: Tue Jul 22 15:10:02 2025
|===========================|
| REGENIE v4.1.gz |
|===========================|
Copyright (c) 2020-2024 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.
Compiled with Boost Iostream library.
Using Intel MKL with Eigen.
Log of output saved in file : ./output/gene_based_testing.log
Options in effect:
--step 2 \
--bed /home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp \
--chr 22 \
--covarFile /home/student/USER/GWAS/data/covar_PCs.txt \
--ref-first \
--phenoFile /home/student/USER/GWAS/data/phenotype.txt \
--strict \
--bsize 1000 \
--apply-rint \
--pred ./output/regenie_step1_W_PC20_pred.list \
--anno-file /home/student/USER/GWAS/data/anno_file.txt \
--set-list /home/student/USER/GWAS/data/set_list.txt \
--mask-def /home/student/USER/GWAS/data/mask_file.txt \
--rgc-gene-p \
--vc-tests skato,acato-full \
--joint acat,sbat \
--vc-MACthr 10 \
--out ./output/gene_based_testing
Association testing mode (joint tests) with fast multithreading using OpenMP
* bim : [/home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp.bim] n_snps = 10396670
* fam : [/home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp.fam] n_samples = 10000
* bed : [/home/student/USER/GWAS/data/v2_backup_20250718/European_1w_imp.bed]
* phenotypes : [/home/student/USER/GWAS/data/phenotype.txt] n_pheno = 1
-dropping observations with missing values at any of the phenotypes
-number of phenotyped individuals with no missing data = 10000
* covariates : [/home/student/USER/GWAS/data/covar_PCs.txt] n_cov = 20
-number of individuals with covariate data = 10000
* number of individuals used in analysis = 10000
-applying RINT to all phenotypes
* number of observations for each trait:
- 'phenotype': 10000 observations
* LOCO predictions : [./output/regenie_step1_W_PC20_pred.list]
-file [/home/tch_lz/./output/regenie_step1_W_PC20_1.loco] for phenotype 'phenotype'
-residualizing and scaling phenotypes...done (0ms)
* annotations : [/home/student/USER/GWAS/data/anno_file.txt]
+number of annotations categories = 6
* masks : [/home/student/USER/GWAS/data/mask_file.txt] n_masks = 7
* aaf cutoffs : [ 4 : 1e-05 0.0001 0.001 0.01 ] + singletons
* set file : [/home/student/USER/GWAS/data/set_list.txt] n_sets = 683
WARNING: Detected 1 sets with variants not in genetic data or annotation files.
* # threads : [31]
* # tested sets : [683]
* max block size : [1000]
* rule used to build masks : max
* computing gene-based tests for each set of variants included in a mask (rho=[0,0.01,0.04,0.09,0.16,0.25,0.5,1])
-variants with MAC <= 10 are collapsed into a mask
-weights are obtained from Beta(MAF,1,25)
-list of gene-based tests run: ACATO,ACATV,SKATO,SKATO-ACAT
* applying ACAT to output overall gene p-value
* approximate memory usage : 222MB
* using minimum MAC of 5 (masks with lower MAC are ignored)
* user specified to test only on select chromosomes
* number of mask groups run through gene-p strategy = 2
* list of joint tests run on burden masks: ACAT,SBAT
Chromosome 22 [683 sets in total]
-reading loco predictions for the chromosome...done (5ms)
set [1/683] : U6 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [2/683] : ABCD1P4 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [3/683] : PABPC1P9 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [4/683] : SLC9B1P4 - 32 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [5/683] : ACTR3BP6 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [6/683] : CHEK2P4 - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [7/683] : KCNMB3P1 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [8/683] : CCT8L2 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [9/683] : TPTEP1 - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [10/683] : SLC25A15P5 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [11/683] : ANKRD62P1 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [12/683] : VWFP1 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [13/683] : ZNF402P - 53 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [14/683] : MTND1P17 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [15/683] : IGKV1OR22-5 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [16/683] : IGKV2OR22-4 - 22 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [17/683] : IGKV2OR22-3 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [18/683] : IGKV3OR22-2 - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [19/683] : IGKV1OR22-1 - 21 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [20/683] : GAB4 - 39 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [21/683] : VN1R9P - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [22/683] : IL17RA - 46 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [23/683] : TMEM121B - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [24/683] : LINC01664 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [25/683] : HDHD5 - 38 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [26/683] : HDHD5-AS1 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [27/683] : ADA2 - 51 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [28/683] : CECR3 - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [29/683] : RN7SL843P - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [30/683] : CECR2 - 358 variants...
-reading in genotypes, computing gene-based tests and building masks...done (8ms)
set [31/683] : SLC25A18 - 34 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [32/683] : ATP6V1E1 - 79 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [33/683] : BCL2L13 - 209 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [34/683] : BID - 55 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [35/683] : LINC00528 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [36/683] : MICAL3 - 496 variants...
-reading in genotypes, computing gene-based tests and building masks...done (11ms)
set [37/683] : LINC01634 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [38/683] : PEX26 - 82 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [39/683] : TUBA8 - 62 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [40/683] : USP18 - 56 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [41/683] : FAM230D - 60 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [42/683] : FAM230A - 83 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [43/683] : GGTLC5P - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [44/683] : FAM230J - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [45/683] : PPP1R26P3 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [46/683] : FAM247B - 81 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [47/683] : GGTLC3 - 45 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [48/683] : TMEM191B - 33 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [49/683] : PI4KAP1 - 106 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [50/683] : RIMBP3 - 22 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [51/683] : Metazoa_SRP - 52 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [52/683] : SUSD2P2 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [53/683] : FAM246B - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [54/683] : CA15P2 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [55/683] : PPP1R26P2 - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [56/683] : PPP1R26P4 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [57/683] : FAM230E - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [58/683] : POM121L15P - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [59/683] : FAM230F - 112 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [60/683] : DGCR6 - 53 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [61/683] : PRODH - 34 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [62/683] : DGCR5 - 41 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [63/683] : CELSR1P1 - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [64/683] : FAM246C - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [65/683] : DGCR2 - 164 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [66/683] : ESS2 - 59 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [67/683] : GSC2 - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [68/683] : LINC01311 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [69/683] : SLC25A1 - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [70/683] : CLTCL1 - 195 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [71/683] : HIRA - 112 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [72/683] : MRPL40 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [73/683] : C22orf39 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [74/683] : UFD1 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [75/683] : CDC45 - 55 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [76/683] : CLDN5 - 14 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [77/683] : LINC00895 - 55 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [78/683] : SEPTIN5 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [79/683] : GP1BB - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [80/683] : TBX1 - 39 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [81/683] : GNB1L - 75 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [82/683] : RTL10 - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [83/683] : TXNRD2 - 146 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [84/683] : COMT - 72 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [85/683] : ARVCF - 64 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [86/683] : TANGO2 - 87 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [87/683] : DGCR8 - 44 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [88/683] : TRMT2A - 28 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [89/683] : RANBP1 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [90/683] : ZDHHC8 - 42 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [91/683] : CCDC188 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [92/683] : LINC02891 - 40 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [93/683] : LINC00896 - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [94/683] : RTN4R - 64 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [95/683] : PRODHLP - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [96/683] : DGCR6L - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [97/683] : FAM230G - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [98/683] : USP41P - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [99/683] : ZNF74 - 14 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [100/683] : SCARF2 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [101/683] : KLHL22 - 25 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [102/683] : MED15 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [103/683] : ABHD17AP4 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [104/683] : POM121L4P - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [105/683] : PI4KA - 234 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [106/683] : SERPIND1 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [107/683] : SNAP29 - 27 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [108/683] : CRKL - 73 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [109/683] : LINC01637 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [110/683] : AIFM3 - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [111/683] : LZTR1 - 22 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [112/683] : THAP7 - 27 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [113/683] : TUBA3FP - 5 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [114/683] : P2RX6 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [115/683] : SLC7A4 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [116/683] : LRRC74B - 58 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [117/683] : E2F6P2 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [118/683] : FAM230B - 39 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [119/683] : FAM247A - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [120/683] : GGT2P - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [121/683] : POM121L8P - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [122/683] : BCRP6 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [123/683] : FAM230H - 46 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [124/683] : PPP1R26P5 - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [125/683] : LINC01651 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [126/683] : FAM246A - 47 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [127/683] : SUSD2P1 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [128/683] : RIMBP3B - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [129/683] : HIC2 - 74 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [130/683] : TMEM191C - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [131/683] : RIMBP3C - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [132/683] : UBE2L3 - 33 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [133/683] : CCDC116 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [134/683] : SDF2L1 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [135/683] : PPIL2 - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [136/683] : YPEL1 - 38 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [137/683] : MAPK1 - 45 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [138/683] : PPM1F - 49 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [139/683] : TOP3B - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [140/683] : PRAMENP - 90 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [141/683] : IGLV4-69 - 22 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [142/683] : IGLVIV-66-1 - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [143/683] : IGLVV-66 - 5 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [144/683] : IGLVIV-65 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [145/683] : IGLVIV-64 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [146/683] : IGLVI-63 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [147/683] : IGLV1-62 - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [148/683] : IGLV8-61 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [149/683] : ABHD17AP5 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [150/683] : IGLV4-60 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [151/683] : SOCS2P2 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [152/683] : IGLVIV-59 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [153/683] : IGLVV-58 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [154/683] : BMP6P1 - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [155/683] : IGLV6-57 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [156/683] : IGLV11-55 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [157/683] : IGLV10-54 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [158/683] : TOP3BP1 - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [159/683] : VPREB1 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [160/683] : BMS1P20 - 22 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [161/683] : IGLV5-52 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [162/683] : IGLV1-51 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [163/683] : IGLV1-50 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [164/683] : ASH2LP3 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [165/683] : IGLV9-49 - 14 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [166/683] : IGLV5-48 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [167/683] : IGLV1-47 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [168/683] : ASH2LP2 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [169/683] : IGLV7-46 - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [170/683] : IGLV5-45 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [171/683] : IGLV1-44 - 24 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [172/683] : IGLV7-43 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [173/683] : IGLV1-41 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [174/683] : IGLV1-40 - 27 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [175/683] : ASH2LP1 - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [176/683] : IGLVI-38 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [177/683] : IGLV5-37 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [178/683] : IGLV1-36 - 27 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [179/683] : ASH2LP4 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [180/683] : IGLV7-35 - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [181/683] : ZNF280B - 84 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [182/683] : ZNF280A - 48 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [183/683] : PRAME - 95 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [184/683] : LL22NC03-63E9.3 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [185/683] : IGLV2-34 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [186/683] : IGLV2-33 - 21 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [187/683] : IGLV3-32 - 51 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [188/683] : IGLV3-31 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [189/683] : IGLV3-30 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [190/683] : BCRP4 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [191/683] : GGTLC2 - 28 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [192/683] : IGLV2-28 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [193/683] : IGLV3-29 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [194/683] : IGLV3-27 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [195/683] : IGLV3-26 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [196/683] : IGLVVI-25-1 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [197/683] : IGLV3-25 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [198/683] : IGLV2-23 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [199/683] : IGLV3-22 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [200/683] : IGLV3-21 - 44 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [201/683] : IGLV3-19 - 27 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [202/683] : IGLV2-18 - 34 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [203/683] : IGLV3-17 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [204/683] : IGLV3-16 - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [205/683] : IGLV3-15 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [206/683] : IGLV2-14 - 30 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [207/683] : IGLV3-13 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [208/683] : IGLV3-12 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [209/683] : IGLV2-11 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [210/683] : IGLV3-10 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [211/683] : IGLV3-9 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [212/683] : IGLV2-8 - 30 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [213/683] : IGLV3-7 - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [214/683] : IGLV3-6 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [215/683] : IGLV2-5 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [216/683] : IGLV3-4 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [217/683] : IGLV4-3 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [218/683] : IGLV3-1 - 24 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [219/683] : IGLL5 - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [220/683] : IGLC2 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [221/683] : IGLC3 - 33 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [222/683] : IGLJ4 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [223/683] : IGLJ5 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [224/683] : IGLJ6 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [225/683] : IGLC7 - 30 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [226/683] : IGLJ7 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [227/683] : ATP5PFP2 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [228/683] : RSPH14 - 74 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [229/683] : GNAZ - 128 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [230/683] : RAB36 - 22 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [231/683] : BCR - 218 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [232/683] : LINC02556 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [233/683] : CES5AP1 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [234/683] : CCDC188BP - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [235/683] : ZDHHC8BP - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [236/683] : LINC01659 - 36 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [237/683] : FAM230I - 62 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [238/683] : LINC02557 - 21 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [239/683] : PCAT14 - 67 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [240/683] : IGLL1 - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [241/683] : DRICH1 - 57 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [242/683] : GUSBP11 - 176 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [243/683] : ASLP1 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [244/683] : RGL4 - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [245/683] : ZNF70 - 89 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [246/683] : VPREB3 - 14 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [247/683] : C22orf15 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [248/683] : CHCHD10 - 25 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [249/683] : MMP11 - 45 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [250/683] : SMARCB1 - 82 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [251/683] : DERL3 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [252/683] : SLC2A11 - 116 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [253/683] : MIF - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [254/683] : MIF-AS1 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [255/683] : KLHL5P1 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [256/683] : GSTT2B - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [257/683] : DDT - 14 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [258/683] : GSTT2 - 30 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [259/683] : GSTT3P - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [260/683] : GSTT4 - 60 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [261/683] : CABIN1 - 310 variants...
-reading in genotypes, computing gene-based tests and building masks...done (5ms)
set [262/683] : SUSD2 - 42 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [263/683] : GGT5 - 77 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [264/683] : POM121L9P - 34 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [265/683] : SPECC1L - 225 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [266/683] : ADORA2A - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [267/683] : ADORA2A-AS1 - 32 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [268/683] : UPB1 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [269/683] : GUCD1 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [270/683] : SNRPD3 - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [271/683] : LRRC75B - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [272/683] : GGT1 - 69 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [273/683] : BCRP3 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [274/683] : POM121L10P - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [275/683] : ARL5AP4 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [276/683] : ACTR2P1 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [277/683] : CRIP1P4 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [278/683] : PIWIL3 - 81 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [279/683] : SGSM1 - 139 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [280/683] : LHFPL7 - 28 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [281/683] : KIAA1671 - 382 variants...
-reading in genotypes, computing gene-based tests and building masks...done (6ms)
set [282/683] : CRYBB3 - 24 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [283/683] : CRYBB2 - 63 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [284/683] : PHF10P2 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [285/683] : CRYBB2P1 - 136 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [286/683] : GRK3-AS1 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [287/683] : GRK3 - 408 variants...
-reading in genotypes, computing gene-based tests and building masks...done (7ms)
set [288/683] : MYO18B - 464 variants...
-reading in genotypes, computing gene-based tests and building masks...done (10ms)
set [289/683] : LINC02559 - 110 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [290/683] : SEZ6L - 352 variants...
-reading in genotypes, computing gene-based tests and building masks...done (6ms)
set [291/683] : RNA5SP495 - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [292/683] : RPS3AP55 - 5 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [293/683] : ASPHD2 - 44 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [294/683] : HPS4 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [295/683] : SRRD - 21 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [296/683] : TFIP11 - 40 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [297/683] : TPST2 - 75 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [298/683] : CRYBB1 - 24 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [299/683] : CRYBA4 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [300/683] : ISCA2P1 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [301/683] : MIAT - 56 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [302/683] : MIATNB - 519 variants...
-reading in genotypes, computing gene-based tests and building masks...done (12ms)
set [303/683] : RNU6-1066P - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [304/683] : LINC01638 - 68 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [305/683] : LINC02554 - 21 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [306/683] : CPMER - 72 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [307/683] : MN1 - 135 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [308/683] : PITPNB - 144 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [309/683] : TTC28-AS1 - 67 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [310/683] : TTC28 - 706 variants...
-reading in genotypes, computing gene-based tests and building masks...done (14ms)
set [311/683] : CHEK2 - 51 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [312/683] : HSCB - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [313/683] : CCDC117 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [314/683] : XBP1 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [315/683] : ZNRF3 - 126 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [316/683] : C22orf31 - 5 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [317/683] : KREMEN1 - 125 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [318/683] : RNU6-1219P - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [319/683] : EMID1 - 74 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [320/683] : RHBDD3 - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [321/683] : EWSR1 - 42 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [322/683] : GAS2L1 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [323/683] : RASL10A - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [324/683] : AP1B1 - 46 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [325/683] : RFPL1S - 87 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [326/683] : RFPL1 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [327/683] : NEFH - 41 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [328/683] : THOC5 - 74 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [329/683] : NIPSNAP1 - 39 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [330/683] : NF2 - 100 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [331/683] : CABP7-DT - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [332/683] : CABP7 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [333/683] : ZMAT5 - 30 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [334/683] : UQCR10 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [335/683] : ASCC2 - 85 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [336/683] : MTMR3 - 184 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [337/683] : HORMAD2-AS1 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [338/683] : HORMAD2 - 109 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [339/683] : LIF - 21 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [340/683] : LIF-AS2 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [341/683] : OSM - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [342/683] : CASTOR1 - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [343/683] : TBC1D10A - 50 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [344/683] : SF3A1 - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [345/683] : CCDC157 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [346/683] : RNF215 - 36 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [347/683] : SEC14L2 - 28 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [348/683] : MTFP1 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [349/683] : SLC39A1P1 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [350/683] : SEC14L3 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [351/683] : SEC14L4 - 30 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [352/683] : SEC14L6 - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [353/683] : GAL3ST1 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [354/683] : PES1 - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [355/683] : TCN2 - 51 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [356/683] : SLC35E4 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [357/683] : RPL13AP26 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [358/683] : DUSP18 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [359/683] : OSBP2 - 263 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [360/683] : MORC2-AS1 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [361/683] : MORC2 - 68 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [362/683] : TUG1 - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [363/683] : SMTN - 41 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [364/683] : SELENOM - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [365/683] : RPS15AP37 - 14 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [366/683] : INPP5J - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [367/683] : PLA2G3 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [368/683] : SNRPNP2 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [369/683] : RNF185 - 72 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [370/683] : LIMK2 - 82 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [371/683] : PIK3IP1 - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [372/683] : PIK3IP1-DT - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [373/683] : PATZ1 - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [374/683] : RNU6-338P - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [375/683] : DRG1 - 33 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [376/683] : EIF4ENIF1 - 99 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [377/683] : SFI1 - 173 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [378/683] : PISD - 46 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [379/683] : PRR14L - 88 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [380/683] : DEPDC5 - 201 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [381/683] : YWHAH-AS1 - 32 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [382/683] : YWHAH - 39 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [383/683] : LINC02558 - 112 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [384/683] : RN7SL305P - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [385/683] : SLC5A1 - 98 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [386/683] : AP1B1P1 - 21 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [387/683] : C22orf42 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [388/683] : RFPL2 - 37 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [389/683] : SLC5A4-AS1 - 35 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [390/683] : SLC5A4 - 45 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [391/683] : RFPL3 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [392/683] : RFPL3S - 27 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [393/683] : RTCB - 59 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [394/683] : BPIFC - 68 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [395/683] : FBXO7 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [396/683] : SYN3 - 1038 variants...
-reading in genotypes, computing gene-based tests and building masks...done (21ms)
set [397/683] : TIMP3 - 111 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [398/683] : LINC01640 - 73 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [399/683] : LARGE1 - 1152 variants...
-reading in genotypes, computing gene-based tests and building masks...done (22ms)
set [400/683] : LARGE1-AS1 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [401/683] : LINC01643 - 287 variants...
-reading in genotypes, computing gene-based tests and building masks...done (5ms)
set [402/683] : ACO2P1 - 30 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [403/683] : LINC02885 - 628 variants...
-reading in genotypes, computing gene-based tests and building masks...done (13ms)
set [404/683] : ISX - 73 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [405/683] : LINC01399 - 211 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [406/683] : HMGXB4 - 61 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [407/683] : TOM1 - 81 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [408/683] : HMOX1 - 30 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [409/683] : MCM5 - 54 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [410/683] : TRMT112P8 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [411/683] : RASD2 - 53 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [412/683] : MB - 35 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [413/683] : APOL6 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [414/683] : MRPS16P3 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [415/683] : APOL5 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [416/683] : RBFOX2 - 473 variants...
-reading in genotypes, computing gene-based tests and building masks...done (10ms)
set [417/683] : APOL3 - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [418/683] : MTCO2P20 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [419/683] : MTATP6P20 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [420/683] : MTCYBP34 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [421/683] : MTND1P10 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [422/683] : APOL4 - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [423/683] : APOL2 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [424/683] : APOL1 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [425/683] : MYH9 - 72 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [426/683] : MYH9-DT - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [427/683] : RPS15AP38 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [428/683] : Y_RNA - 44 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [429/683] : TXN2 - 25 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [430/683] : FOXRED2 - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [431/683] : EIF3D - 36 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [432/683] : CACNG2 - 380 variants...
-reading in genotypes, computing gene-based tests and building masks...done (6ms)
set [433/683] : CACNG2-DT - 47 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [434/683] : IFT27 - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [435/683] : PVALB - 46 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [436/683] : NCF4-AS1 - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [437/683] : NCF4 - 52 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [438/683] : CSF2RB - 99 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [439/683] : LL22NC01-81G9.3 - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [440/683] : CIMIP4 - 25 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [441/683] : TST - 24 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [442/683] : MPST - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [443/683] : KCTD17 - 28 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [444/683] : TMPRSS6 - 83 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [445/683] : IL2RB - 56 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [446/683] : C1QTNF6 - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [447/683] : SSTR3 - 25 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [448/683] : RPL39P41 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [449/683] : RAC2 - 60 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [450/683] : CYTH4 - 72 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [451/683] : ELFN2 - 202 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [452/683] : MFNG - 42 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [453/683] : CARD10 - 57 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [454/683] : CDC42EP1 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [455/683] : LGALS2 - 39 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [456/683] : GGA1 - 63 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [457/683] : SH3BP1 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [458/683] : PDXP - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [459/683] : LGALS1 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [460/683] : NOL12 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [461/683] : TRIOBP - 132 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [462/683] : H1-0 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [463/683] : GCAT - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [464/683] : GALR3 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [465/683] : ANKRD54 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [466/683] : EIF3L - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [467/683] : MICALL1 - 80 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [468/683] : C22orf23 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [469/683] : POLR2F - 63 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [470/683] : SOX10 - 39 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [471/683] : MIR4534 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [472/683] : PICK1 - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [473/683] : BAIAP2L2 - 53 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [474/683] : PLA2G6 - 82 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [475/683] : MAFF - 25 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [476/683] : TMEM184B - 56 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [477/683] : CSNK1E - 40 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [478/683] : KCNJ4 - 32 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [479/683] : KDELR3 - 28 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [480/683] : DDX17 - 25 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [481/683] : DMC1 - 109 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [482/683] : FAM227A - 116 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [483/683] : CBY1 - 28 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [484/683] : TOMM22 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [485/683] : JOSD1 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [486/683] : GTPBP1 - 32 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [487/683] : SUN2 - 33 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [488/683] : DNAL4 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [489/683] : NPTXR - 48 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [490/683] : CBX6 - 25 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [491/683] : APOBEC3A - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [492/683] : APOBEC3B - 22 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [493/683] : APOBEC3B-AS1 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [494/683] : APOBEC3C - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [495/683] : APOBEC3D - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [496/683] : APOBEC3F - 50 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [497/683] : APOBEC3G - 22 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [498/683] : APOBEC3H - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [499/683] : COX5BP7 - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [500/683] : CBX7 - 28 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [501/683] : PDGFB - 50 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [502/683] : RPL3 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [503/683] : SYNGR1 - 58 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [504/683] : TAB1 - 76 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [505/683] : MGAT3 - 75 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [506/683] : MIEF1 - 50 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [507/683] : ATF4 - 2 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [508/683] : RPS19BP1 - 16 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [509/683] : CACNA1I - 239 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [510/683] : ENTHD1 - 174 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [511/683] : GRAP2 - 69 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [512/683] : FAM83F - 56 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [513/683] : TNRC6B-DT - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [514/683] : TNRC6B - 151 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [515/683] : RPL7P52 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [516/683] : ADSL - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [517/683] : SGSM3 - 37 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [518/683] : MRTFA - 227 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [519/683] : GAPDHP37 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [520/683] : MCHR1 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [521/683] : SLC25A17 - 34 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [522/683] : ST13 - 25 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [523/683] : XPNPEP3 - 65 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [524/683] : RBX1 - 27 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [525/683] : RPS9P2 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [526/683] : ACTBP15 - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [527/683] : EP300 - 166 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [528/683] : EP300-AS1 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [529/683] : L3MBTL2 - 24 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [530/683] : CHADL - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [531/683] : RANGAP1 - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [532/683] : ZC3H7B - 35 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [533/683] : TEF - 41 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [534/683] : TOB2 - 42 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [535/683] : ACO2 - 40 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [536/683] : PHF5A - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [537/683] : POLR3H - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [538/683] : CSDC2 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [539/683] : PMM1 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [540/683] : DESI1 - 33 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [541/683] : XRCC6 - 70 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [542/683] : SNU13 - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [543/683] : C22orf46P - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [544/683] : MEI1 - 120 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [545/683] : CCDC134 - 35 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [546/683] : SREBF2 - 72 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [547/683] : SHISA8 - 5 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [548/683] : TNFRSF13C - 15 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [549/683] : CENPM - 21 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [550/683] : SMIM45 - 19 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [551/683] : SEPTIN3 - 22 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [552/683] : WBP2NL - 70 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [553/683] : NAGA - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [554/683] : PHETA2 - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [555/683] : SMDT1 - 5 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [556/683] : NDUFA6 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [557/683] : NDUFA6-DT - 33 variants...
-reading in genotypes, computing gene-based tests and building masks...done (5ms)
set [558/683] : CYP2D6 - 34 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [559/683] : CYP2D7 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [560/683] : CYP2D8P - 14 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [561/683] : TCF20 - 256 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [562/683] : OGFRP1 - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [563/683] : LINC01315 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [564/683] : NFAM1 - 84 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [565/683] : SERHL - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [566/683] : RRP7A - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [567/683] : SERHL2 - 37 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [568/683] : POLDIP3 - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [569/683] : CYB5R3 - 59 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [570/683] : ATP5MGL - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [571/683] : A4GALT - 57 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [572/683] : RPL5P34 - 33 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [573/683] : GOLGA2P4 - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [574/683] : ARFGAP3 - 84 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [575/683] : PACSIN2 - 251 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [576/683] : TTLL1-AS1 - 21 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [577/683] : TTLL1 - 127 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [578/683] : RPS25P10 - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [579/683] : BIK - 42 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [580/683] : MCAT - 40 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [581/683] : TSPO - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [582/683] : TTLL12 - 79 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [583/683] : SCUBE1 - 226 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [584/683] : LINC01639 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [585/683] : MPPED1 - 216 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [586/683] : EFCAB6-AS1 - 11 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [587/683] : EFCAB6 - 507 variants...
-reading in genotypes, computing gene-based tests and building masks...done (22ms)
set [588/683] : EFCAB6-DT - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [589/683] : SULT4A1 - 84 variants...
-reading in genotypes, computing gene-based tests and building masks...done (5ms)
set [590/683] : PNPLA5 - 37 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [591/683] : PNPLA3 - 40 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [592/683] : SAMM50 - 72 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [593/683] : PARVB - 250 variants...
-reading in genotypes, computing gene-based tests and building masks...done (9ms)
set [594/683] : PARVG - 56 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [595/683] : SHISAL1 - 133 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [596/683] : SKP1P4 - 9 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [597/683] : LINC01656 - 10 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [598/683] : MRPS18CP6 - 6 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [599/683] : RTL6 - 40 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [600/683] : KRT18P23 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [601/683] : LINC00207 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [602/683] : LINC00229 - 78 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [603/683] : ANP32BP2 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [604/683] : PRR5 - 138 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [605/683] : ARHGAP8 - 296 variants...
-reading in genotypes, computing gene-based tests and building masks...done (6ms)
set [606/683] : PHF21B - 288 variants...
-reading in genotypes, computing gene-based tests and building masks...done (5ms)
set [607/683] : NUP50-DT - 109 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [608/683] : NUP50 - 113 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [609/683] : KIAA0930 - 169 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [610/683] : UPK3A - 40 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [611/683] : FAM118A - 82 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [612/683] : SMC1B - 69 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [613/683] : RIBC2 - 73 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [614/683] : FBLN1 - 217 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [615/683] : LINC01589 - 57 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [616/683] : ATXN10 - 239 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [617/683] : WNT7B - 149 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [618/683] : LINC00899 - 14 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [619/683] : PRR34 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [620/683] : MIRLET7BHG - 59 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [621/683] : LINC02939 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [622/683] : MIR3619 - 1 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [623/683] : PPARA - 131 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [624/683] : CDPF1 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [625/683] : PKDREJ - 7 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [626/683] : TTC38 - 51 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [627/683] : GTSE1 - 123 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [628/683] : TRMU - 55 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [629/683] : CELSR1 - 239 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [630/683] : LINC02925 - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [631/683] : GRAMD4 - 157 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [632/683] : CERK - 118 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [633/683] : TBC1D22A - 908 variants...
-reading in genotypes, computing gene-based tests and building masks...done (22ms)
set [634/683] : LINC01644 - 209 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [635/683] : LINC00898 - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [636/683] : EPIC1 - 541 variants...
-reading in genotypes, computing gene-based tests and building masks...done (18ms)
set [637/683] : MIR3201 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [638/683] : TAFA5 - 817 variants...
-reading in genotypes, computing gene-based tests and building masks...done (17ms)
set [639/683] : MIR4535 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [640/683] : LINC01310 - 92 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [641/683] : NHIP - 81 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [642/683] : RPL35P8 - 33 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [643/683] : MIR3667HG - 801 variants...
-reading in genotypes, computing gene-based tests and building masks...done (17ms)
set [644/683] : RN7SKP252 - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [645/683] : RPL5P35 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [646/683] : BRD1 - 210 variants...
-reading in genotypes, computing gene-based tests and building masks...done (4ms)
set [647/683] : ZBED4 - 94 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [648/683] : ALG12 - 61 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [649/683] : CRELD2 - 34 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [650/683] : PIM3 - 32 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [651/683] : IL17REL - 45 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [652/683] : TTLL8 - 84 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [653/683] : MLC1 - 73 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [654/683] : MOV10L1 - 149 variants...
-reading in genotypes, computing gene-based tests and building masks...done (3ms)
set [655/683] : PANX2 - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [656/683] : TRABD - 23 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [657/683] : SELENOO - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [658/683] : TUBGCP6 - 64 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [659/683] : HDAC10 - 17 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [660/683] : MAPK12 - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [661/683] : MAPK11 - 43 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [662/683] : PLXNB2 - 68 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [663/683] : DENND6B - 85 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [664/683] : PPP6R2 - 99 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [665/683] : SBF1 - 96 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [666/683] : ADM2 - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [667/683] : MIOX - 18 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [668/683] : LMF2 - 76 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [669/683] : NCAPH2 - 13 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [670/683] : SCO2 - 26 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [671/683] : TYMP - 8 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [672/683] : CIMAP1B - 4 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [673/683] : KLHDC7B - 12 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [674/683] : SYCE3 - 44 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [675/683] : CPT1B - 42 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [676/683] : CHKB - 20 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [677/683] : CHKB-DT - 14 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [678/683] : MAPK8IP2 - 46 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [679/683] : ARSA - 29 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [680/683] : SHANK3 - 122 variants...
-reading in genotypes, computing gene-based tests and building masks...done (2ms)
set [681/683] : ACR - 31 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
set [682/683] : SNRPA1P2 - 3 variants...
-reading in genotypes, computing gene-based tests and building masks...done (0ms)
set [683/683] : RABL2B - 58 variants...
-reading in genotypes, computing gene-based tests and building masks...done (1ms)
Association results stored separately for each trait in files :
* [./output/gene_based_testing_phenotype.regenie]
Number of ignored tests due to low MAC : 0
Elapsed time : 10.3566s
End time: Tue Jul 22 15:10:12 2025
(regenie_env)
For each set, this will produce masks using 3 AAF cutoffs (singletons, 5% and 10% AAF).
The masks are written to PLINK bed file (in _masks.{bed,bim,fam}) and tested for association with each trait (summary stats in _phenotype_name.regenie).
Additionally, a header line is included (starting with ##) which contains mask definition information.
Masks will have name set_name.mask_name.AAF_cutoff with the chromosome and physical position having been defined in the set list file, and the reference allele being ref, and the alternate allele corresponding to mask_name.AAF_cutoff.
When using --rgc-gene-p, it will apply the single p-value per gene GENE_P strategy using all masks.
Excercise F: Calculate GWAS power¶
Now we generate a statistical power analysis plot for GWAS studies.
Supports binary (case-control) traits over a range of odds ratios and minor allele frequencies, and quantitative traits over a range of effect sizes and minor allele frequencies.
Part1 : Quantitative traits¶
In our above example, standing height is the quantitative trait.
# calculate the standard deviation of the quantitative trait
import pandas as pd
df = pd.read_table(
'/home/student/USER/GWAS/data/European_1w_phenotypes.txt',
sep = '\\s+',
header = 0
)
print(df.shape)
df['Standing_height'].std(skipna=True)
(10000, 11)
np.float64(0.09365788681305078)
options(repr.plot.width = 16,
repr.plot.height = 8,
repr.plot.res = 600)
source("/home/student/USER/GWAS/data/plotPlink.R")
power_results_qt <- plot_gwas_power(
trait_type = "qt",
sd_trait = 0.09365788681305078,
N = 10000,
maf_levels = c(0.01, 0.02, 0.05, 0.10, 0.20, 0.50),
effect_size = seq(0.01, 0.10, 0.001),
save_plot = FALSE
)
print(power_results_qt$plot)
Part2: Binary traits¶
Now we generate a statistical power analysis plot for a given range of odds ratios and minor allele frequencies in a case-control GWAS study.
Statistical power is crucial for designing a successful GWAS.
It helps you determine the probability of detecting a true association, given a specific sample size, allele frequency, and effect size (Odds Ratio).
Example Usage¶
Let's run the example with a sample dataset:
Cases: 4,324
Controls: 93,945
Odds Ratios: Ranging from 1.01 to 2.00
MAF: 0.01, 0.02, 0.05, 0.10, 0.20, 0.50
options(repr.plot.width = 16,
repr.plot.height = 8,
repr.plot.res = 600)
source("/home/student/USER/GWAS/data/plotPlink.R")
power_results <- plot_gwas_power(
trait_type = "bt",
n_cases = 4324,
n_controls = 93945,
maf_levels = c(0.01, 0.02, 0.05, 0.10, 0.20, 0.50),
or_range = seq(1.01, 2.00, 0.01),
save_plot = FALSE
)
print(power_results$plot)